NM_014173.4:c.837G>A

Variant names:

• chr19-17278895-G-A
• rs8170
• NM_014173.4:c.837G>A

Variant summary

Our verdict is Benign. The variant received -11 ACMG points: 0P and 11B. BP4_Moderate BP7 BA1

The NM_014173.4(BABAM1):​c.837G>A​(p.Lys279Lys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.174 in 1,613,148 control chromosomes in the GnomAD database, including 25,760 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 0.17 (2472 hom., cov: 32)
  • Exomes 𝑓: 0.17 (23288 hom.)
• Consequence: BABAM1 NM_014173.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.06
• Publications: 175 publications found

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]

ENSG00000269307 (HGNC:):

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

Our verdict: Benign. The variant received -11 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.42).
• BP7: Synonymous conserved (PhyloP=3.06 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.188 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014173.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BABAM1	NM_014173.4	MANE Select	c.837G>A	p.Lys279Lys	synonymous	Exon 9 of 9	NP_054892.2	Q9NWV8-1
	BABAM1	NM_001033549.3		c.837G>A	p.Lys279Lys	synonymous	Exon 9 of 9	NP_001028721.1	Q9NWV8-1
	BABAM1	NM_001288756.2		c.837G>A	p.Lys279Lys	synonymous	Exon 9 of 9	NP_001275685.1	Q9NWV8-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BABAM1	ENST00000598188.6	TSL:1 MANE Select	c.837G>A	p.Lys279Lys	synonymous	Exon 9 of 9	ENSP00000471605.1	Q9NWV8-1
	BABAM1	ENST00000359435.8	TSL:1	c.837G>A	p.Lys279Lys	synonymous	Exon 9 of 9	ENSP00000352408.3	Q9NWV8-1
	ENSG00000269307	ENST00000596542.1	TSL:2	n.*400+1986G>A		intron	N/A	ENSP00000469159.2	M0QXG9

Frequencies

GnomAD3 genomes AF: 0.173 AC: 26386 AN: 152088 Hom.: 2466 Cov.: 32

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.0855

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.238

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.163

GnomAD2 exomes AF: 0.149 AC: 36995 AN: 247668 AF XY: 0.151

Gnomad AFR exome AF: 0.192

Gnomad AMR exome AF: 0.0800

Gnomad ASJ exome AF: 0.162

Gnomad EAS exome AF: 0.000613

Gnomad FIN exome AF: 0.241

Gnomad NFE exome AF: 0.179

Gnomad OTH exome AF: 0.151

GnomAD4 exome AF: 0.174 AC: 253709 AN: 1460942 Hom.: 23288 Cov.: 33 AF XY: 0.173 AC XY: 125471 AN XY: 726676

African (AFR) AF: 0.190 AC: 6345 AN: 33474

American (AMR) AF: 0.0837 AC: 3737 AN: 44652

Ashkenazi Jewish (ASJ) AF: 0.172 AC: 4486 AN: 26108

East Asian (EAS) AF: 0.000504 AC: 20 AN: 39694

South Asian (SAS) AF: 0.118 AC: 10195 AN: 86170

European-Finnish (FIN) AF: 0.238 AC: 12652 AN: 53210

Middle Eastern (MID) AF: 0.102 AC: 590 AN: 5762

European-Non Finnish (NFE) AF: 0.185 AC: 205895 AN: 1111518

Other (OTH) AF: 0.162 AC: 9789 AN: 60354

GnomAD4 genome AF: 0.174 AC: 26410 AN: 152206 Hom.: 2472 Cov.: 32 AF XY: 0.171 AC XY: 12751 AN XY: 74390

African (AFR) AF: 0.192 AC: 7957 AN: 41532

American (AMR) AF: 0.108 AC: 1648 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.173 AC: 599 AN: 3472

East Asian (EAS) AF: 0.00154 AC: 8 AN: 5180

South Asian (SAS) AF: 0.107 AC: 518 AN: 4830

European-Finnish (FIN) AF: 0.238 AC: 2516 AN: 10580

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.187 AC: 12720 AN: 68000

Other (OTH) AF: 0.161 AC: 340 AN: 2116

Alfa AF: 0.175 Hom.: 11453

Bravo AF: 0.164

Asia WGS AF: 0.0610 AC: 215 AN: 3478

EpiCase AF: 0.175

EpiControl AF: 0.170

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.42
CADD	Benign	11
DANN	Benign	0.86
PhyloP100		3.1
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs8170; hg19: chr19-17389704; COSMIC: COSV63920809; COSMIC: COSV63920809;