dbSNP rs78904893: BSND:c.177+11G>A (chr1-54999374-G-A) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_057176.3(BSND):c.177+11G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0336 in 1,600,054 control chromosomes in the GnomAD database, including 2,557 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.068 ( 612 hom., cov: 32)

Exomes 𝑓: 0.030 ( 1945 hom. )

Consequence

BSND
NM_057176.3 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:8

Conservation

PhyloP100: -0.532

Variant links:

Genes affected

BSND (HGNC:16512): (barttin CLCNK type accessory subunit beta) This gene encodes an essential beta subunit for CLC chloride channels. These heteromeric channels localize to basolateral membranes of renal tubules and of potassium-secreting epithelia of the inner ear. Mutations in this gene have been associated with Bartter syndrome with sensorineural deafness. [provided by RefSeq, Jul 2008]

BSND links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.62).

BP6

Variant 1-54999374-G-A is Benign according to our data. Variant chr1-54999374-G-A is described in ClinVar as [Benign]. Clinvar id is 46546.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-54999374-G-A is described in Lovd as [Likely_benign].

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.145 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BSND	NM_057176.3 link	c.177+11G>A		intron_variant	Intron 1 of 3	ENST00000651561.1	NP_476517.1	Q8WZ55Q5VU50

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BSND	ENST00000651561.1 link	c.177+11G>A		intron_variant	Intron 1 of 3		NM_057176.3	ENSP00000498282.1		Q8WZ55

Frequencies

GnomAD3 genomes

AF:

0.0680

AC:

10337

AN:

152120

Hom.:

609

Cov.:

show subpopulations

Gnomad AFR

AF:

0.149

Gnomad AMI

AF:

0.0208

Gnomad AMR

AF:

0.101

Gnomad ASJ

AF:

0.0490

Gnomad EAS

AF:

0.125

Gnomad SAS

AF:

0.0739

Gnomad FIN

AF:

0.0214

Gnomad MID

AF:

0.123

Gnomad NFE

AF:

0.0152

Gnomad OTH

AF:

0.0742

GnomAD3 exomes

AF:

0.0643

AC:

15698

AN:

244242

Hom.:

940

AF XY:

0.0576

AC XY:

7594

AN XY:

131880

show subpopulations

Gnomad AFR exome

AF:

0.151

Gnomad AMR exome

AF:

0.168

Gnomad ASJ exome

AF:

0.0494

Gnomad EAS exome

AF:

0.125

Gnomad SAS exome

AF:

0.0704

Gnomad FIN exome

AF:

0.0236

Gnomad NFE exome

AF:

0.0168

Gnomad OTH exome

AF:

0.0578

GnomAD4 exome

AF:

0.0300

AC:

43374

AN:

1447818

Hom.:

1945

Cov.:

AF XY:

0.0303

AC XY:

21762

AN XY:

717690

show subpopulations

Gnomad4 AFR exome

AF:

0.154

Gnomad4 AMR exome

AF:

0.159

Gnomad4 ASJ exome

AF:

0.0499

Gnomad4 EAS exome

AF:

0.144

Gnomad4 SAS exome

AF:

0.0686

Gnomad4 FIN exome

AF:

0.0241

Gnomad4 NFE exome

AF:

0.0127

Gnomad4 OTH exome

AF:

0.0450

GnomAD4 genome

AF:

0.0681

AC:

10361

AN:

152236

Hom.:

612

Cov.:

AF XY:

0.0685

AC XY:

5099

AN XY:

74438

show subpopulations

Gnomad4 AFR

AF:

0.148

Gnomad4 AMR

AF:

0.101

Gnomad4 ASJ

AF:

0.0490

Gnomad4 EAS

AF:

0.126

Gnomad4 SAS

AF:

0.0740

Gnomad4 FIN

AF:

0.0214

Gnomad4 NFE

AF:

0.0152

Gnomad4 OTH

AF:

0.0739

Alfa

AF:

0.0338

Hom.:

Bravo

AF:

0.0806

Asia WGS

AF:

0.102

AC:

354

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:8

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:3

Apr 29, 2016

Eurofins Ntd Llc (ga)

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Apr 30, 2012

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

177+11G>A in Intron 01 of BSND: This variant is not expected to have clinical si gnificance because it is not located within the conserved splice consensus seque nce and has been identified in 14.5% (543/3738) of African American chromosomes from a broad population by the NHLBI Exome Sequencing Project (http://evs.gs.was hington.edu/EVS; dbSNP rs78904893). -

not provided

Benign:3

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Jul 05, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Bartter disease type 4A

Benign:2

Jul 10, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jan 12, 2018

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.62

CADD

Benign

9.9

DANN

Benign

0.82

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over