chr6-2959279-C-T

Variant names:

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_004568.6(SERPINB6):c.54G>A(p.Thr18Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.317 in 1,613,822 control chromosomes in the GnomAD database, including 83,768 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.30 ( 7294 hom., cov: 32)

Exomes 𝑓: 0.32 ( 76474 hom. )

Consequence

SERPINB6
NM_004568.6 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: -1.58

Variant links:

Genes affected

SERPINB6 (HGNC:8950): (serpin family B member 6) The protein encoded by this gene is a member of the serpin (serine proteinase inhibitor) superfamily, and ovalbumin(ov)-serpin subfamily. It was originally discovered as a placental thrombin inhibitor. The mouse homolog was found to be expressed in the hair cells of the inner ear. Mutations in this gene are associated with nonsyndromic progressive hearing loss, suggesting that this serpin plays an important role in the inner ear in the protection against leakage of lysosomal content during stress, and that loss of this protection results in cell death and sensorineural hearing loss. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Sep 2010]

SERPINB6 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.54).

BP6

Variant 6-2959279-C-T is Benign according to our data. Variant chr6-2959279-C-T is described in ClinVar as [Benign]. Clinvar id is 44135.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-2959279-C-T is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=-1.58 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.484 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SERPINB6	NM_004568.6 link	c.54G>A	p.Thr18Thr	synonymous_variant	Exon 2 of 7	ENST00000380539.7	NP_004559.4	P35237A0A024QZX3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SERPINB6	ENST00000380539.7 link	c.54G>A	p.Thr18Thr	synonymous_variant	Exon 2 of 7	3	NM_004568.6	ENSP00000369912.2		P35237

Frequencies

GnomAD3 genomes

AF:

0.296

AC:

44912

AN:

151954

Hom.:

7291

Cov.:

show subpopulations

Gnomad AFR

AF:

0.183

Gnomad AMI

AF:

0.363

Gnomad AMR

AF:

0.388

Gnomad ASJ

AF:

0.373

Gnomad EAS

AF:

0.500

Gnomad SAS

AF:

0.356

Gnomad FIN

AF:

0.277

Gnomad MID

AF:

0.377

Gnomad NFE

AF:

0.320

Gnomad OTH

AF:

0.338

GnomAD3 exomes

AF:

0.349

AC:

87707

AN:

251466

Hom.:

16340

AF XY:

0.344

AC XY:

46740

AN XY:

135908

show subpopulations

Gnomad AFR exome

AF:

0.174

Gnomad AMR exome

AF:

0.495

Gnomad ASJ exome

AF:

0.380

Gnomad EAS exome

AF:

0.501

Gnomad SAS exome

AF:

0.335

Gnomad FIN exome

AF:

0.278

Gnomad NFE exome

AF:

0.319

Gnomad OTH exome

AF:

0.346

GnomAD4 exome

AF:

0.319

AC:

466494

AN:

1461752

Hom.:

76474

Cov.:

AF XY:

0.319

AC XY:

232322

AN XY:

727186

show subpopulations

Gnomad4 AFR exome

AF:

0.168

Gnomad4 AMR exome

AF:

0.481

Gnomad4 ASJ exome

AF:

0.375

Gnomad4 EAS exome

AF:

0.498

Gnomad4 SAS exome

AF:

0.334

Gnomad4 FIN exome

AF:

0.282

Gnomad4 NFE exome

AF:

0.310

Gnomad4 OTH exome

AF:

0.322

GnomAD4 genome

AF:

0.295

AC:

44914

AN:

152070

Hom.:

7294

Cov.:

AF XY:

0.296

AC XY:

21996

AN XY:

74340

show subpopulations

Gnomad4 AFR

AF:

0.182

Gnomad4 AMR

AF:

0.388

Gnomad4 ASJ

AF:

0.373

Gnomad4 EAS

AF:

0.500

Gnomad4 SAS

AF:

0.355

Gnomad4 FIN

AF:

0.277

Gnomad4 NFE

AF:

0.320

Gnomad4 OTH

AF:

0.336

Alfa

AF:

0.325

Hom.:

13729

Bravo

AF:

0.303

Asia WGS

AF:

0.387

AC:

1342

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:3

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

May 07, 2012

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Thr18Thr in Exon 03 of SERPINB6: This variant is not expected to have clinical significance because it does not alter an amino acid residue, is not located wit hin the splice consensus sequence, and has been identified in 32.1% (2253/7020) of European American chromosomes from a broad population by the NHLBI Exome Sequ encing Project (http://evs.gs.washington.edu/EVS; dbSNP rs2236277). -

May 09, 2017

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Autosomal recessive nonsyndromic hearing loss 91

Benign:1

Jul 15, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided

Benign:1

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.54

CADD

Benign

8.1

DANN

Benign

0.62

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.10

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