7-7690080-C-G

Variant names:

• chr7-7690080-C-G
• rs2108003
• NM_001302348.2:c.82+16627C>G

Variant summary

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

The NM_001302348.2(UMAD1):​c.82+16627C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.575 in 151,910 control chromosomes in the GnomAD database, including 25,384 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 (25384 hom., cov: 31)
• Consequence: UMAD1 NM_001302348.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.60
• Publications: 4 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.781 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UMAD1	NM_001302348.2	c.82+16627C>G		intron_variant	Intron 2 of 3	ENST00000682710.1	NP_001289277.1
RPA3	NM_002947.5	c.-1027-2752G>C		intron_variant	Intron 2 of 7	ENST00000223129.8	NP_002938.1
UMAD1	NM_001302349.2	c.82+16627C>G		intron_variant	Intron 2 of 3		NP_001289278.1
UMAD1	NM_001302350.2	c.-24+13872C>G		intron_variant	Intron 3 of 4		NP_001289279.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UMAD1	ENST00000682710.1	c.82+16627C>G		intron_variant	Intron 2 of 3		NM_001302348.2	ENSP00000507605.1
RPA3	ENST00000223129.8	c.-1027-2752G>C		intron_variant	Intron 2 of 7	1	NM_002947.5	ENSP00000223129.4

Frequencies

GnomAD3 genomes AF: 0.576 AC: 87363 AN: 151792 Hom.: 25370 Cov.: 31

Gnomad AFR AF: 0.523

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.625

Gnomad ASJ AF: 0.585

Gnomad EAS AF: 0.801

Gnomad SAS AF: 0.588

Gnomad FIN AF: 0.601

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.577

Gnomad OTH AF: 0.547

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

GnomAD4 genome AF: 0.575 AC: 87409 AN: 151910 Hom.: 25384 Cov.: 31 AF XY: 0.578 AC XY: 42928 AN XY: 74222

African (AFR) AF: 0.523 AC: 21664 AN: 41428

American (AMR) AF: 0.625 AC: 9537 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.585 AC: 2029 AN: 3470

East Asian (EAS) AF: 0.801 AC: 4147 AN: 5176

South Asian (SAS) AF: 0.588 AC: 2829 AN: 4814

European-Finnish (FIN) AF: 0.601 AC: 6333 AN: 10536

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.577 AC: 39215 AN: 67910

Other (OTH) AF: 0.546 AC: 1154 AN: 2114

Alfa AF: 0.478 Hom.: 1441

Bravo AF: 0.578

Asia WGS AF: 0.631 AC: 2193 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.068
DANN	Benign	0.54
PhyloP100		-1.6
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: rs2108003; hg19: chr7-7729711;