Variant 17-81443902-G-T 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.2309G>T(p.Arg770Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00458 in 711,620 control chromosomes in the GnomAD database, including 10 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0040 ( 2 hom., cov: 34)

Exomes 𝑓: 0.0047 ( 8 hom. )

Consequence

BAHCC1
NM_001377448.1 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 2.34

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=0.0070741475).

BP6

Variant 17-81443902-G-T is Benign according to our data. Variant chr17-81443902-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 2648450.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd at 2 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BAHCC1	NM_001377448.1 linkuse as main transcript	c.2309G>T	p.Arg770Leu	missense_variant	6/28	ENST00000675386.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris
BAHCC1	ENST00000675386.2 linkuse as main transcript	c.2309G>T	p.Arg770Leu	missense_variant	6/28		NM_001377448.1	P2
BAHCC1	ENST00000584436.7 linkuse as main transcript	c.2309G>T	p.Arg770Leu	missense_variant	6/29	5		A2
BAHCC1	ENST00000585224.1 linkuse as main transcript	n.194G>T		non_coding_transcript_exon_variant	2/2	5

Frequencies

GnomAD3 genomes

AF:

0.00405

AC:

616

AN:

152234

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00164

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00373

Gnomad ASJ

AF:

0.000864

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.00124

Gnomad FIN

AF:

0.00790

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00576

Gnomad OTH

AF:

0.00239

GnomAD3 exomes

AF:

0.00397

AC:

590

AN:

148662

Hom.:

AF XY:

0.00394

AC XY:

312

AN XY:

79144

show subpopulations

Gnomad AFR exome

AF:

0.00153

Gnomad AMR exome

AF:

0.00239

Gnomad ASJ exome

AF:

0.00106

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00119

Gnomad FIN exome

AF:

0.00805

Gnomad NFE exome

AF:

0.00649

Gnomad OTH exome

AF:

0.00326

GnomAD4 exome

AF:

0.00473

AC:

2645

AN:

559268

Hom.:

Cov.:

AF XY:

0.00464

AC XY:

1401

AN XY:

302226

show subpopulations

Gnomad4 AFR exome

AF:

0.00139

Gnomad4 AMR exome

AF:

0.00205

Gnomad4 ASJ exome

AF:

0.000600

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00150

Gnomad4 FIN exome

AF:

0.00750

Gnomad4 NFE exome

AF:

0.00623

Gnomad4 OTH exome

AF:

0.00496

GnomAD4 genome

AF:

0.00404

AC:

616

AN:

152352

Hom.:

Cov.:

AF XY:

0.00413

AC XY:

308

AN XY:

74496

show subpopulations

Gnomad4 AFR

AF:

0.00164

Gnomad4 AMR

AF:

0.00372

Gnomad4 ASJ

AF:

0.000864

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.00124

Gnomad4 FIN

AF:

0.00790

Gnomad4 NFE

AF:

0.00576

Gnomad4 OTH

AF:

0.00236

Alfa

AF:

0.00409

Hom.:

Bravo

AF:

0.00334

TwinsUK

AF:

0.00836

AC:

ALSPAC

AF:

0.00545

AC:

ESP6500AA

AF:

0.00105

AC:

ESP6500EA

AF:

0.00599

AC:

ExAC

AF:

0.00140

AC:

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

Jan 01, 2023

BAHCC1: BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

0.71

BayesDel_addAF

Benign

-0.40

BayesDel_noAF

Benign

-0.34

Cadd

Benign

Dann

Uncertain

1.0

DEOGEN2

Uncertain

0.47

T;T

Eigen

Benign

0.096

Eigen_PC

Benign

-0.086

FATHMM_MKL

Benign

0.52

LIST_S2

Benign

0.85

T;T

M_CAP

Benign

0.072

MetaRNN

Benign

0.0071

T;T

MetaSVM

Benign

-0.81

MutationAssessor

Uncertain

2.3

M;.

MutationTaster

Benign

0.80

PrimateAI

Uncertain

0.70

Sift4G

Uncertain

0.010

D;D

Polyphen

0.99

D;.

Vest4

0.52

MVP

0.17

MPC

0.25

ClinPred

0.025

GERP RS

4.3

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.20

gMVP

0.21

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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