Variant 17-81445621-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_001377448.1(BAHCC1):c.3103G>A(p.Ala1035Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00111 in 732,424 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00048 ( 0 hom., cov: 33)

Exomes 𝑓: 0.0013 ( 8 hom. )

Consequence

BAHCC1
NM_001377448.1 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.32

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 -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.004210353).

BP6

Variant 17-81445621-G-A is Benign according to our data. Variant chr17-81445621-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2648451.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAdExome4 at 8 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BAHCC1	NM_001377448.1 link	c.3103G>A	p.Ala1035Thr	missense_variant	10/28	ENST00000675386.2	NP_001364377.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BAHCC1	ENST00000675386.2 link	c.3103G>A	p.Ala1035Thr	missense_variant	10/28		NM_001377448.1	ENSP00000502710.1		F8WBW8
BAHCC1	ENST00000584436.7 link	c.3103G>A	p.Ala1035Thr	missense_variant	10/29	5		ENSP00000462154.4		Q9P281

Frequencies

GnomAD3 genomes

AF:

0.000473

AC:

AN:

152090

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000262

Gnomad ASJ

AF:

0.000288

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00683

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.000441

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.00155

AC:

268

AN:

173092

Hom.:

AF XY:

0.00205

AC XY:

191

AN XY:

93310

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.000486

Gnomad ASJ exome

AF:

0.00149

Gnomad EAS exome

AF:

0.0000795

Gnomad SAS exome

AF:

0.00806

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000636

Gnomad OTH exome

AF:

0.00106

GnomAD4 exome

AF:

0.00128

AC:

742

AN:

580218

Hom.:

Cov.:

AF XY:

0.00170

AC XY:

534

AN XY:

313904

show subpopulations

Gnomad4 AFR exome

AF:

0.000182

Gnomad4 AMR exome

AF:

0.000518

Gnomad4 ASJ exome

AF:

0.00153

Gnomad4 EAS exome

AF:

0.0000904

Gnomad4 SAS exome

AF:

0.00765

Gnomad4 FIN exome

AF:

0.0000414

Gnomad4 NFE exome

AF:

0.000429

Gnomad4 OTH exome

AF:

0.000927

GnomAD4 genome

AF:

0.000480

AC:

AN:

152206

Hom.:

Cov.:

AF XY:

0.000591

AC XY:

AN XY:

74420

show subpopulations

Gnomad4 AFR

AF:

0.00

Gnomad4 AMR

AF:

0.000261

Gnomad4 ASJ

AF:

0.000288

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00704

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000441

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.000559

Hom.:

Bravo

AF:

0.000321

ESP6500AA

AF:

0.00

AC:

ESP6500EA

AF:

0.000379

AC:

ExAC

AF:

0.000999

AC:

115

Asia WGS

AF:

0.00231

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

Jul 01, 2022

BAHCC1: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.070

BayesDel_addAF

Benign

-0.66

BayesDel_noAF

Benign

-0.71

CADD

Benign

0.11

DANN

Benign

0.90

DEOGEN2

Benign

0.083

T;T

Eigen

Benign

-1.6

Eigen_PC

Benign

-1.6

FATHMM_MKL

Benign

0.061

LIST_S2

Benign

0.43

T;T

MetaRNN

Benign

0.0042

T;T

MetaSVM

Benign

-0.97

MutationAssessor

Benign

0.46

N;.

PrimateAI

Benign

0.28

PROVEAN

Benign

-0.010

.;N

REVEL

Benign

0.013

Sift

Benign

1.0

.;T

Sift4G

Benign

0.64

T;T

Polyphen

0.0020

B;B

Vest4

0.075

MVP

0.014

MPC

0.082

ClinPred

0.0089

GERP RS

-3.9

Varity_R

0.016

gMVP

0.097

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