Variant rs10406920 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_014173.4(BABAM1):c.787-6C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 1,608,172 control chromosomes in the GnomAD database, including 25,508 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.17 ( 2410 hom., cov: 32)

Exomes 𝑓: 0.17 ( 23098 hom. )

Consequence

BABAM1
NM_014173.4 splice_region, intron

Scores

Splicing: ADA: 0.00002312

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.798

Variant links:

Genes affected

BABAM1 (HGNC:25008): (BRISC and BRCA1 A complex member 1) Involved in several processes, including mitotic G2 DNA damage checkpoint signaling; positive regulation of DNA repair; and protein K63-linked deubiquitination. Located in cytosol and nuclear body. Part of BRCA1-A complex and BRISC complex. [provided by Alliance of Genome Resources, Apr 2022]

BABAM1 links:

ENSG00000269307 (HGNC:):

ENSG00000269307 links:

USHBP1 (HGNC:24058): (USH1 protein network component harmonin binding protein 1) Enables PDZ domain binding activity. [provided by Alliance of Genome Resources, Apr 2022]

USHBP1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.79).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.184 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein	UniProt
BABAM1	NM_014173.4 linkuse as main transcript	c.787-6C>T	splice_region_variant, intron_variant	ENST00000598188.6	NP_054892.2	Q9NWV8-1A0A024R7L2
BABAM1	NM_001033549.3 linkuse as main transcript	c.787-6C>T	splice_region_variant, intron_variant		NP_001028721.1	Q9NWV8-1A0A024R7L2
BABAM1	NM_001288756.2 linkuse as main transcript	c.787-6C>T	splice_region_variant, intron_variant		NP_001275685.1	Q9NWV8-1A0A024R7L2
BABAM1	NM_001288757.2 linkuse as main transcript	c.562-6C>T	splice_region_variant, intron_variant		NP_001275686.1	Q9NWV8J3KQS6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BABAM1	ENST00000598188.6 linkuse as main transcript	c.787-6C>T		splice_region_variant, intron_variant		1	NM_014173.4	ENSP00000471605.1		Q9NWV8-1
ENSG00000269307	ENST00000596542.1 linkuse as main transcript	n.*400+1930C>T		intron_variant		2		ENSP00000469159.2		M0QXG9

Frequencies

GnomAD3 genomes

AF:

0.172

AC:

26092

AN:

152062

Hom.:

2411

Cov.:

show subpopulations

Gnomad AFR

AF:

0.185

Gnomad AMI

AF:

0.0855

Gnomad AMR

AF:

0.107

Gnomad ASJ

AF:

0.173

Gnomad EAS

AF:

0.00154

Gnomad SAS

AF:

0.108

Gnomad FIN

AF:

0.238

Gnomad MID

AF:

0.0886

Gnomad NFE

AF:

0.187

Gnomad OTH

AF:

0.159

GnomAD3 exomes

AF:

0.147

AC:

35422

AN:

240154

Hom.:

3021

AF XY:

0.150

AC XY:

19548

AN XY:

130652

show subpopulations

Gnomad AFR exome

AF:

0.183

Gnomad AMR exome

AF:

0.0790

Gnomad ASJ exome

AF:

0.161

Gnomad EAS exome

AF:

0.000562

Gnomad SAS exome

AF:

0.114

Gnomad FIN exome

AF:

0.240

Gnomad NFE exome

AF:

0.178

Gnomad OTH exome

AF:

0.150

GnomAD4 exome

AF:

0.173

AC:

252053

AN:

1455992

Hom.:

23098

Cov.:

AF XY:

0.172

AC XY:

124619

AN XY:

723778

show subpopulations

Gnomad4 AFR exome

AF:

0.182

Gnomad4 AMR exome

AF:

0.0825

Gnomad4 ASJ exome

AF:

0.172

Gnomad4 EAS exome

AF:

0.000505

Gnomad4 SAS exome

AF:

0.118

Gnomad4 FIN exome

AF:

0.237

Gnomad4 NFE exome

AF:

0.185

Gnomad4 OTH exome

AF:

0.161

GnomAD4 genome

AF:

0.171

AC:

26089

AN:

152180

Hom.:

2410

Cov.:

AF XY:

0.170

AC XY:

12611

AN XY:

74398

show subpopulations

Gnomad4 AFR

AF:

0.185

Gnomad4 AMR

AF:

0.107

Gnomad4 ASJ

AF:

0.173

Gnomad4 EAS

AF:

0.00154

Gnomad4 SAS

AF:

0.108

Gnomad4 FIN

AF:

0.238

Gnomad4 NFE

AF:

0.187

Gnomad4 OTH

AF:

0.157

Alfa

AF:

0.175

Hom.:

1766

Bravo

AF:

0.161

Asia WGS

AF:

0.0570

AC:

202

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

3.4

DANN

Benign

0.38

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.000023

dbscSNV1_RF

Benign

0.0020

SpliceAI score (max)

0.010

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over