7-7652246-G-T

Variant names:

• chr7-7652246-G-T
• rs7783714
• NM_001302348.2:c.-64+11425G>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.-64+11425G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.734 in 152,096 control chromosomes in the GnomAD database, including 41,293 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 0.73 (41293 hom., cov: 32)
• Consequence: UMAD1 NM_001302348.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.432
• Publications: 5 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.948 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UMAD1	NM_001302348.2	c.-64+11425G>T		intron_variant	Intron 1 of 3	ENST00000682710.1	NP_001289277.1
RPA3	NM_002947.5	c.-757-11071C>A		intron_variant	Intron 4 of 7	ENST00000223129.8	NP_002938.1
UMAD1	NM_001302349.2	c.-57+11425G>T		intron_variant	Intron 1 of 3		NP_001289278.1
UMAD1	NM_001302350.2	c.-276+11425G>T		intron_variant	Intron 1 of 4		NP_001289279.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UMAD1	ENST00000682710.1	c.-64+11425G>T		intron_variant	Intron 1 of 3		NM_001302348.2	ENSP00000507605.1
RPA3	ENST00000223129.8	c.-757-11071C>A		intron_variant	Intron 4 of 7	1	NM_002947.5	ENSP00000223129.4

Frequencies

GnomAD3 genomes AF: 0.734 AC: 111588 AN: 151978 Hom.: 41256 Cov.: 32

Gnomad AFR AF: 0.728

Gnomad AMI AF: 0.497

Gnomad AMR AF: 0.755

Gnomad ASJ AF: 0.755

Gnomad EAS AF: 0.970

Gnomad SAS AF: 0.780

Gnomad FIN AF: 0.786

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.707

Gnomad OTH AF: 0.721

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

GnomAD4 genome AF: 0.734 AC: 111672 AN: 152096 Hom.: 41293 Cov.: 32 AF XY: 0.740 AC XY: 55015 AN XY: 74366

African (AFR) AF: 0.727 AC: 30157 AN: 41462

American (AMR) AF: 0.755 AC: 11537 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.755 AC: 2619 AN: 3470

East Asian (EAS) AF: 0.971 AC: 5035 AN: 5188

South Asian (SAS) AF: 0.780 AC: 3758 AN: 4820

European-Finnish (FIN) AF: 0.786 AC: 8304 AN: 10562

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.707 AC: 48080 AN: 67996

Other (OTH) AF: 0.722 AC: 1524 AN: 2112

Alfa AF: 0.726 Hom.: 19135

Bravo AF: 0.731

Asia WGS AF: 0.855 AC: 2976 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.4
DANN	Benign	0.79
PhyloP100		-0.43
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: rs7783714; hg19: chr7-7691877;