Variant chr17-81459100-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_001377448.1(BAHCC1):c.5652C>T(p.Pro1884Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00105 in 771,080 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00081 ( 0 hom., cov: 34)

Exomes 𝑓: 0.0011 ( 2 hom. )

Consequence

BAHCC1
NM_001377448.1 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -3.27

Variant links:

Genes affected

BAHCC1 (HGNC:29279): (BAH domain and coiled-coil containing 1) Predicted to enable chromatin binding activity. [provided by Alliance of Genome Resources, Apr 2022]

BAHCC1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.68).

BP6

Variant 17-81459100-C-T is Benign according to our data. Variant chr17-81459100-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2648454.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-3.27 with no splicing effect.

BS2

High Homozygotes in GnomAdExome4 at 2 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BAHCC1	NM_001377448.1 link	c.5652C>T	p.Pro1884Pro	synonymous_variant	21/28	ENST00000675386.2	NP_001364377.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BAHCC1	ENST00000675386.2 link	c.5652C>T	p.Pro1884Pro	synonymous_variant	21/28		NM_001377448.1	ENSP00000502710.1		F8WBW8
BAHCC1	ENST00000584436.7 link	c.5745C>T	p.Pro1915Pro	synonymous_variant	22/29	5		ENSP00000462154.4		Q9P281

Frequencies

GnomAD3 genomes

AF:

0.000808

AC:

123

AN:

152194

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000217

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000654

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.00165

Gnomad FIN

AF:

0.000188

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00132

Gnomad OTH

AF:

0.000957

GnomAD3 exomes

AF:

0.000932

AC:

216

AN:

231864

Hom.:

AF XY:

0.000944

AC XY:

120

AN XY:

127138

show subpopulations

Gnomad AFR exome

AF:

0.000301

Gnomad AMR exome

AF:

0.000391

Gnomad ASJ exome

AF:

0.000104

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000964

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00157

Gnomad OTH exome

AF:

0.000878

GnomAD4 exome

AF:

0.00111

AC:

689

AN:

618768

Hom.:

Cov.:

AF XY:

0.00116

AC XY:

390

AN XY:

336976

show subpopulations

Gnomad4 AFR exome

AF:

0.000229

Gnomad4 AMR exome

AF:

0.000420

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0000281

Gnomad4 SAS exome

AF:

0.00112

Gnomad4 FIN exome

AF:

0.000179

Gnomad4 NFE exome

AF:

0.00154

Gnomad4 OTH exome

AF:

0.00113

GnomAD4 genome

AF:

0.000808

AC:

123

AN:

152312

Hom.:

Cov.:

AF XY:

0.000792

AC XY:

AN XY:

74476

show subpopulations

Gnomad4 AFR

AF:

0.000217

Gnomad4 AMR

AF:

0.000653

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.00166

Gnomad4 FIN

AF:

0.000188

Gnomad4 NFE

AF:

0.00132

Gnomad4 OTH

AF:

0.000947

Alfa

AF:

0.000732

Hom.:

Bravo

AF:

0.000929

Asia WGS

AF:

0.00115

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Oct 01, 2022

BAHCC1: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.68

CADD

Benign

0.23

DANN

Benign

0.93

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