Variant chr17-81458716-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7

The NM_001377448.1(BAHCC1):c.5439C>T(p.Ala1813=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000264 in 732,038 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00022 ( 0 hom., cov: 35)

Exomes 𝑓: 0.00028 ( 0 hom. )

Consequence

BAHCC1
NM_001377448.1 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.702

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 Likely_benign. Variant got -5 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.74).

BP6

Variant 17-81458716-C-T is Benign according to our data. Variant chr17-81458716-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2648452.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.702 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BAHCC1	NM_001377448.1 linkuse as main transcript	c.5439C>T	p.Ala1813=	synonymous_variant	19/28	ENST00000675386.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BAHCC1	ENST00000675386.2 linkuse as main transcript	c.5439C>T	p.Ala1813=	synonymous_variant	19/28		NM_001377448.1	P2
BAHCC1	ENST00000584436.7 linkuse as main transcript	c.5532C>T	p.Ala1844=	synonymous_variant	20/29	5		A2

Frequencies

GnomAD3 genomes

AF:

0.000217

AC:

AN:

152172

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000483

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000131

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000207

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000382

Gnomad OTH

AF:

0.000956

GnomAD3 exomes

AF:

0.000344

AC:

AN:

174562

Hom.:

AF XY:

0.000384

AC XY:

AN XY:

93686

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.000423

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000291

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000526

Gnomad OTH exome

AF:

0.000849

GnomAD4 exome

AF:

0.000276

AC:

160

AN:

579866

Hom.:

Cov.:

AF XY:

0.000268

AC XY:

AN XY:

313700

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.000444

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0000300

Gnomad4 SAS exome

AF:

0.000265

Gnomad4 FIN exome

AF:

0.0000206

Gnomad4 NFE exome

AF:

0.000347

Gnomad4 OTH exome

AF:

0.000383

GnomAD4 genome

AF:

0.000217

AC:

AN:

152172

Hom.:

Cov.:

AF XY:

0.000229

AC XY:

AN XY:

74336

show subpopulations

Gnomad4 AFR

AF:

0.0000483

Gnomad4 AMR

AF:

0.000131

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000207

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000382

Gnomad4 OTH

AF:

0.000956

Alfa

AF:

0.000292

Hom.:

Bravo

AF:

0.000302

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, 2022

BAHCC1: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.74

CADD

Benign

2.3

DANN

Benign

0.81

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