Variant chr17-81447231-T-C 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.3359T>C(p.Leu1120Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0043 in 730,508 control chromosomes in the GnomAD database, including 23 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0038 ( 4 hom., cov: 31)

Exomes 𝑓: 0.0044 ( 19 hom. )

Consequence

BAHCC1
NM_001377448.1 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.306

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=0.0031389594).

BP6

Variant 17-81447231-T-C is Benign according to our data. Variant chr17-81447231-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 3025095.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 4 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BAHCC1	NM_001377448.1 link	c.3359T>C	p.Leu1120Pro	missense_variant	11/28	ENST00000675386.2	NP_001364377.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BAHCC1	ENST00000675386.2 link	c.3359T>C	p.Leu1120Pro	missense_variant	11/28		NM_001377448.1	ENSP00000502710.1		F8WBW8
BAHCC1	ENST00000584436.7 link	c.3452T>C	p.Leu1151Pro	missense_variant	12/29	5		ENSP00000462154.4		Q9P281

Frequencies

GnomAD3 genomes

AF:

0.00383

AC:

583

AN:

152026

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000411

Gnomad AMI

AF:

0.0593

Gnomad AMR

AF:

0.000458

Gnomad ASJ

AF:

0.00202

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000207

Gnomad FIN

AF:

0.0283

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00281

Gnomad OTH

AF:

0.00287

GnomAD3 exomes

AF:

0.00498

AC:

897

AN:

179976

Hom.:

AF XY:

0.00449

AC XY:

445

AN XY:

99204

show subpopulations

Gnomad AFR exome

AF:

0.000788

Gnomad AMR exome

AF:

0.000593

Gnomad ASJ exome

AF:

0.00261

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0000971

Gnomad FIN exome

AF:

0.0318

Gnomad NFE exome

AF:

0.00336

Gnomad OTH exome

AF:

0.00703

GnomAD4 exome

AF:

0.00443

AC:

2560

AN:

578364

Hom.:

Cov.:

AF XY:

0.00392

AC XY:

1232

AN XY:

313972

show subpopulations

Gnomad4 AFR exome

AF:

0.000754

Gnomad4 AMR exome

AF:

0.000846

Gnomad4 ASJ exome

AF:

0.00242

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000970

Gnomad4 FIN exome

AF:

0.0307

Gnomad4 NFE exome

AF:

0.00259

Gnomad4 OTH exome

AF:

0.00377

GnomAD4 genome

AF:

0.00383

AC:

582

AN:

152144

Hom.:

Cov.:

AF XY:

0.00458

AC XY:

341

AN XY:

74382

show subpopulations

Gnomad4 AFR

AF:

0.000410

Gnomad4 AMR

AF:

0.000458

Gnomad4 ASJ

AF:

0.00202

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000207

Gnomad4 FIN

AF:

0.0283

Gnomad4 NFE

AF:

0.00280

Gnomad4 OTH

AF:

0.00284

Alfa

AF:

0.00199

Hom.:

Bravo

AF:

0.00198

TwinsUK

AF:

0.00135

AC:

ALSPAC

AF:

0.00234

AC:

ESP6500AA

AF:

0.000588

AC:

ESP6500EA

AF:

0.00181

AC:

ExAC

AF:

0.00395

AC:

464

Asia WGS

AF:

0.000577

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

Dec 01, 2023

BAHCC1: BP4 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.063

BayesDel_addAF

Benign

-0.50

BayesDel_noAF

Benign

-0.50

CADD

Benign

DANN

Benign

0.75

DEOGEN2

Benign

0.23

T;T

Eigen

Benign

-1.0

Eigen_PC

Benign

-1.0

FATHMM_MKL

Benign

0.020

LIST_S2

Benign

0.54

T;T

MetaRNN

Benign

0.0031

T;T

MetaSVM

Benign

-1.0

PrimateAI

Benign

0.47

PROVEAN

Benign

-0.13

.;N

REVEL

Benign

0.071

Sift

Benign

0.22

.;T

Sift4G

Benign

0.30

T;T

Polyphen

0.0010

.;B

Vest4

0.028

MVP

0.076

MPC

0.14

ClinPred

0.00057

GERP RS

1.9

Varity_R

0.053

gMVP

0.22

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