rs61634114

chr19-17276445-G-A

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.653

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]

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

ACMG classification

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	HGVSp	Effect	#exon/exons	MANE	UniProt
BABAM1	NM_014173.4	c.570-50G>A		intron_variant		ENST00000598188.6
BABAM1	NM_001033549.3	c.570-50G>A		intron_variant
BABAM1	NM_001288756.2	c.570-50G>A		intron_variant
BABAM1	NM_001288757.2	c.345-50G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BABAM1	ENST00000598188.6	c.570-50G>A		intron_variant		1	NM_014173.4	P1

Frequencies

GnomAD3 genomes AF: 0.160 AC: 24247 AN: 151922 Hom.: 2114 Cov.: 32

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

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.: 32 AF XY: 0.172 AC XY: 119744 AN XY: 695872

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.: 32 AF XY: 0.158 AC XY: 11706 AN XY: 74296

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

Other links and lift over

dbSNP: rs61634114; hg19: chr19-17387254;