rs2073802959

Variant names:

• chr19-17268882-C-A
• NM_014173.4:c.76C>A

Your query was ambiguous. Multiple possible variants found:

• chr19-17268882-C-A
• chr19-17268882-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_014173.4(BABAM1):​c.76C>A​(p.Arg26Ser) variant causes a missense change. The variant allele was found at a frequency of 0.000000692 in 1,444,112 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R26C) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 31)
  • Exomes 𝑓: 6.9e-7 (0 hom.)
• Consequence: BABAM1 NM_014173.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.58

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

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.21563464).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BABAM1	NM_014173.4	c.76C>A	p.Arg26Ser	missense_variant	Exon 2 of 9	ENST00000598188.6	NP_054892.2
BABAM1	NM_001033549.3	c.76C>A	p.Arg26Ser	missense_variant	Exon 2 of 9		NP_001028721.1
BABAM1	NM_001288756.2	c.76C>A	p.Arg26Ser	missense_variant	Exon 2 of 9		NP_001275685.1
BABAM1	NM_001288757.2	c.76C>A	p.Arg26Ser	missense_variant	Exon 2 of 6		NP_001275686.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BABAM1	ENST00000598188.6	c.76C>A	p.Arg26Ser	missense_variant	Exon 2 of 9	1	NM_014173.4	ENSP00000471605.1
ENSG00000269307	ENST00000596542.1	n.76C>A		non_coding_transcript_exon_variant	Exon 2 of 10	2		ENSP00000469159.2

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome AF: 6.92e-7 AC: 1 AN: 1444112 Hom.: 0 Cov.: 31 AF XY: 0.00000140 AC XY: 1 AN XY: 716766

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 9.06e-7

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.23
BayesDel_addAF	Benign	-0.019	T
BayesDel_noAF	Benign	-0.27
CADD	Uncertain	24
DANN	Uncertain	1.0
DEOGEN2	Benign	0.036	T;T;T;T;.;T;T;.;T;.;.
Eigen	Benign	-0.0082
Eigen_PC	Benign	0.037
FATHMM_MKL	Uncertain	0.95	D
LIST_S2	Uncertain	0.94	.;D;.;D;D;D;D;D;.;D;D
M_CAP	Benign	0.0081	T
MetaRNN	Benign	0.22	T;T;T;T;T;T;T;T;T;T;T
MetaSVM	Benign	-0.69	T
MutationAssessor	Uncertain	2.2	M;.;M;.;.;M;.;.;.;.;.
PrimateAI	Uncertain	0.58	T
PROVEAN	Benign	-1.4	.;N;N;.;.;.;.;.;.;.;.
REVEL	Benign	0.024
Sift	Uncertain	0.014	.;D;D;.;.;.;.;.;.;.;.
Sift4G	Uncertain	0.037	D;D;D;D;D;D;D;D;D;D;D
Polyphen		0.14	B;.;B;.;.;B;.;.;.;.;.
Vest4		0.30
MutPred		0.21		Gain of phosphorylation at R26 (P = 5e-04);Gain of phosphorylation at R26 (P = 5e-04);Gain of phosphorylation at R26 (P = 5e-04);Gain of phosphorylation at R26 (P = 5e-04);Gain of phosphorylation at R26 (P = 5e-04);Gain of phosphorylation at R26 (P = 5e-04);Gain of phosphorylation at R26 (P = 5e-04);Gain of phosphorylation at R26 (P = 5e-04);Gain of phosphorylation at R26 (P = 5e-04);.;Gain of phosphorylation at R26 (P = 5e-04);
MVP		0.23
MPC		0.52
ClinPred		0.89	D
GERP RS		3.8
RBP_binding_hub_radar		0.97
RBP_regulation_power_radar		2.1
Varity_R		0.34
gMVP		0.46

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr19-17379691;