chr7-7665508-C-T

Variant names:

• chr7-7665508-C-T
• rs6974820
• NM_001302348.2:c.-63-7801C>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.-63-7801C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.197 in 152,110 control chromosomes in the GnomAD database, including 3,161 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 0.20 (3161 hom., cov: 33)
• Consequence: UMAD1 NM_001302348.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.406
• Publications: 2 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.217 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.-63-7801C>T		intron	N/A	NP_001289277.1	C9J7I0
	RPA3	NM_002947.5	MANE Select	c.-758+20322G>A		intron	N/A	NP_002938.1	P35244
	UMAD1	NM_001302349.2		c.-56-7808C>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.-63-7801C>T		intron	N/A	ENSP00000507605.1	C9J7I0
	RPA3	ENST00000223129.8	TSL:1 MANE Select	c.-758+20322G>A		intron	N/A	ENSP00000223129.4	P35244
	UMAD1	ENST00000949980.1		c.-63-7801C>T		intron	N/A	ENSP00000620039.1

Frequencies

GnomAD3 genomes AF: 0.197 AC: 29976 AN: 151992 Hom.: 3156 Cov.: 33

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.00982

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.197 AC: 29993 AN: 152110 Hom.: 3161 Cov.: 33 AF XY: 0.192 AC XY: 14269 AN XY: 74352

African (AFR) AF: 0.221 AC: 9168 AN: 41482

American (AMR) AF: 0.167 AC: 2552 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.190 AC: 661 AN: 3472

East Asian (EAS) AF: 0.00965 AC: 50 AN: 5184

South Asian (SAS) AF: 0.157 AC: 755 AN: 4820

European-Finnish (FIN) AF: 0.148 AC: 1569 AN: 10574

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.213 AC: 14485 AN: 67972

Other (OTH) AF: 0.212 AC: 447 AN: 2112

Alfa AF: 0.112 Hom.: 188

Bravo AF: 0.199

Asia WGS AF: 0.0860 AC: 300 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	8.9
DANN	Benign	0.45
PhyloP100		0.41
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: rs6974820; hg19: chr7-7705139;