rs2057931

Variant names:

• chr7-7670110-C-T
• rs2057931
• NM_001302348.2:c.-63-3199C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001302348.2(UMAD1):​c.-63-3199C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.581 in 151,986 control chromosomes in the GnomAD database, including 25,916 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 0.58 (25916 hom., cov: 32)
• Consequence: UMAD1 NM_001302348.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0140
• Publications: 3 publications found

Genes affected

UMAD1 (HGNC:48955): (UBAP1-MVB12-associated (UMA) domain containing 1)

RPA3 (HGNC:10291): (replication protein A3) Enables damaged DNA binding activity and single-stranded DNA binding activity. Involved in DNA repair and DNA replication. Part of DNA replication factor A complex. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000283549 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.779 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001302348.2. 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
	UMAD1	NM_001302348.2	MANE Select	c.-63-3199C>T		intron	N/A	NP_001289277.1	C9J7I0
	RPA3	NM_002947.5	MANE Select	c.-758+15720G>A		intron	N/A	NP_002938.1	P35244
	UMAD1	NM_001302349.2		c.-56-3206C>T		intron	N/A	NP_001289278.1	C9J7I0

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UMAD1	ENST00000682710.1	MANE Select	c.-63-3199C>T		intron	N/A	ENSP00000507605.1	C9J7I0
	RPA3	ENST00000223129.8	TSL:1 MANE Select	c.-758+15720G>A		intron	N/A	ENSP00000223129.4	P35244
	UMAD1	ENST00000949980.1		c.-63-3199C>T		intron	N/A	ENSP00000620039.1

Frequencies

GnomAD3 genomes AF: 0.581 AC: 88260 AN: 151868 Hom.: 25899 Cov.: 32

Gnomad AFR AF: 0.530

Gnomad AMI AF: 0.387

Gnomad AMR AF: 0.634

Gnomad ASJ AF: 0.594

Gnomad EAS AF: 0.799

Gnomad SAS AF: 0.577

Gnomad FIN AF: 0.611

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.582

Gnomad OTH AF: 0.550

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.581 AC: 88312 AN: 151986 Hom.: 25916 Cov.: 32 AF XY: 0.584 AC XY: 43382 AN XY: 74288

African (AFR) AF: 0.530 AC: 21951 AN: 41400

American (AMR) AF: 0.635 AC: 9709 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.594 AC: 2058 AN: 3466

East Asian (EAS) AF: 0.799 AC: 4125 AN: 5162

South Asian (SAS) AF: 0.576 AC: 2782 AN: 4828

European-Finnish (FIN) AF: 0.611 AC: 6450 AN: 10562

Middle Eastern (MID) AF: 0.507 AC: 148 AN: 292

European-Non Finnish (NFE) AF: 0.582 AC: 39577 AN: 67960

Other (OTH) AF: 0.549 AC: 1160 AN: 2114

Alfa AF: 0.591 Hom.: 3319

Bravo AF: 0.583

Asia WGS AF: 0.628 AC: 2186 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.95
DANN	Benign	0.55
PhyloP100		-0.014
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: rs2057931; hg19: chr7-7709741;