dbSNP rs61634114: BABAM1:c.570-50G>A (chr19-17276445-G-A) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_014173.4(BABAM1):c.570-50G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 1,560,662 control chromosomes in the GnomAD database, including 24,334 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.16 ( 2113 hom., cov: 32)

Exomes 𝑓: 0.17 ( 22221 hom. )

Consequence

BABAM1
NM_014173.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.653

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 -8 ACMG points.

BA1

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
BABAM1	NM_014173.4 link	c.570-50G>A	intron_variant	Intron 6 of 8	ENST00000598188.6	NP_054892.2	Q9NWV8-1A0A024R7L2
BABAM1	NM_001033549.3 link	c.570-50G>A	intron_variant	Intron 6 of 8		NP_001028721.1	Q9NWV8-1A0A024R7L2
BABAM1	NM_001288756.2 link	c.570-50G>A	intron_variant	Intron 6 of 8		NP_001275685.1	Q9NWV8-1A0A024R7L2
BABAM1	NM_001288757.2 link	c.345-50G>A	intron_variant	Intron 3 of 5		NP_001275686.1	Q9NWV8J3KQS6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BABAM1	ENST00000598188.6 link	c.570-50G>A		intron_variant	Intron 6 of 8	1	NM_014173.4	ENSP00000471605.1		Q9NWV8-1
ENSG00000269307	ENST00000596542.1 link	n.*184-50G>A		intron_variant	Intron 5 of 9	2		ENSP00000469159.2		M0QXG9

Frequencies

GnomAD3 genomes

AF:

0.160

AC:

24247

AN:

151922

Hom.:

2114

Cov.:

show subpopulations

Gnomad AFR

AF:

0.144

Gnomad AMI

AF:

0.0848

Gnomad AMR

AF:

0.103

Gnomad ASJ

AF:

0.168

Gnomad EAS

AF:

0.00154

Gnomad SAS

AF:

0.107

Gnomad FIN

AF:

0.238

Gnomad MID

AF:

0.0886

Gnomad NFE

AF:

0.187

Gnomad OTH

AF:

0.152

GnomAD3 exomes

AF:

0.145

AC:

24702

AN:

170148

Hom.:

2126

AF XY:

0.147

AC XY:

13377

AN XY:

90976

show subpopulations

Gnomad AFR exome

AF:

0.145

Gnomad AMR exome

AF:

0.0815

Gnomad ASJ exome

AF:

0.158

Gnomad EAS exome

AF:

0.000666

Gnomad SAS exome

AF:

0.117

Gnomad FIN exome

AF:

0.243

Gnomad NFE exome

AF:

0.178

Gnomad OTH exome

AF:

0.154

GnomAD4 exome

AF:

0.173

AC:

243646

AN:

1408622

Hom.:

22221

Cov.:

AF XY:

0.172

AC XY:

119744

AN XY:

695872

show subpopulations

Gnomad4 AFR exome

AF:

0.136

Gnomad4 AMR exome

AF:

0.0842

Gnomad4 ASJ exome

AF:

0.169

Gnomad4 EAS exome

AF:

0.000551

Gnomad4 SAS exome

AF:

0.119

Gnomad4 FIN exome

AF:

0.238

Gnomad4 NFE exome

AF:

0.185

Gnomad4 OTH exome

AF:

0.158

GnomAD4 genome

AF:

0.159

AC:

24240

AN:

152040

Hom.:

2113

Cov.:

AF XY:

0.158

AC XY:

11706

AN XY:

74296

show subpopulations

Gnomad4 AFR

AF:

0.143

Gnomad4 AMR

AF:

0.102

Gnomad4 ASJ

AF:

0.168

Gnomad4 EAS

AF:

0.00155

Gnomad4 SAS

AF:

0.107

Gnomad4 FIN

AF:

0.238

Gnomad4 NFE

AF:

0.187

Gnomad4 OTH

AF:

0.149

Alfa

AF:

0.177

Hom.:

710

Bravo

AF:

0.148

Asia WGS

AF:

0.0540

AC:

189

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

9.6

DANN

Benign

0.67

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.23

Details are displayed if max score is > 0.2

DS_AG_spliceai

0.23

Position offset: -12

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