7-7652852-G-T

Variant names:

• chr7-7652852-G-T
• rs886724
• NM_001302348.2:c.-64+12031G>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+12031G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.344 in 152,126 control chromosomes in the GnomAD database, including 10,015 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 0.34 (10015 hom., cov: 33)
• Consequence: UMAD1 NM_001302348.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00100
• 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=-0.9).
• 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UMAD1	NM_001302348.2	MANE Select	c.-64+12031G>T		intron	N/A	NP_001289277.1
	RPA3	NM_002947.5	MANE Select	c.-757-11677C>A		intron	N/A	NP_002938.1
	UMAD1	NM_001302349.2		c.-57+12031G>T		intron	N/A	NP_001289278.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UMAD1	ENST00000682710.1	MANE Select	c.-64+12031G>T		intron	N/A	ENSP00000507605.1
	RPA3	ENST00000223129.8	TSL:1 MANE Select	c.-757-11677C>A		intron	N/A	ENSP00000223129.4
	UMAD1	ENST00000636849.1	TSL:5	c.-51+12031G>T		intron	N/A	ENSP00000489648.1

Frequencies

GnomAD3 genomes AF: 0.345 AC: 52373 AN: 152008 Hom.: 10008 Cov.: 33

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.799

Gnomad SAS AF: 0.482

Gnomad FIN AF: 0.444

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.364

Gnomad OTH AF: 0.320

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

GnomAD4 genome AF: 0.344 AC: 52402 AN: 152126 Hom.: 10015 Cov.: 33 AF XY: 0.352 AC XY: 26171 AN XY: 74374

African (AFR) AF: 0.216 AC: 8951 AN: 41500

American (AMR) AF: 0.349 AC: 5337 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.323 AC: 1122 AN: 3470

East Asian (EAS) AF: 0.799 AC: 4144 AN: 5184

South Asian (SAS) AF: 0.483 AC: 2332 AN: 4830

European-Finnish (FIN) AF: 0.444 AC: 4689 AN: 10562

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.364 AC: 24766 AN: 67978

Other (OTH) AF: 0.325 AC: 685 AN: 2108

Alfa AF: 0.352 Hom.: 15800

Bravo AF: 0.330

Asia WGS AF: 0.589 AC: 2047 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.7
DANN	Benign	0.74
PhyloP100		-0.0010
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: rs886724; hg19: chr7-7692483; COSMIC: COSV56189717;