7-7716166-T-C

Variant names:

• chr7-7716166-T-C
• rs2160138
• NM_001302348.2:c.82+42713T>C

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+42713T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.409 in 151,968 control chromosomes in the GnomAD database, including 13,201 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 0.41 (13201 hom., cov: 31)
• Consequence: UMAD1 NM_001302348.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.769
• Publications: 6 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=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.46 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.82+42713T>C		intron	N/A	NP_001289277.1	C9J7I0
	RPA3	NM_002947.5	MANE Select	c.-1079-940A>G		intron	N/A	NP_002938.1	P35244
	UMAD1	NM_001302349.2		c.82+42713T>C		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.82+42713T>C		intron	N/A	ENSP00000507605.1	C9J7I0
	RPA3	ENST00000223129.8	TSL:1 MANE Select	c.-1079-940A>G		intron	N/A	ENSP00000223129.4	P35244
	UMAD1	ENST00000949980.1		c.189+39958T>C		intron	N/A	ENSP00000620039.1

Frequencies

GnomAD3 genomes AF: 0.409 AC: 62104 AN: 151850 Hom.: 13186 Cov.: 31

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.615

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.517

Gnomad EAS AF: 0.195

Gnomad SAS AF: 0.414

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.464

Gnomad OTH AF: 0.444

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

GnomAD4 genome AF: 0.409 AC: 62154 AN: 151968 Hom.: 13201 Cov.: 31 AF XY: 0.406 AC XY: 30115 AN XY: 74260

African (AFR) AF: 0.333 AC: 13790 AN: 41438

American (AMR) AF: 0.386 AC: 5888 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.517 AC: 1790 AN: 3464

East Asian (EAS) AF: 0.195 AC: 1012 AN: 5180

South Asian (SAS) AF: 0.415 AC: 2002 AN: 4822

European-Finnish (FIN) AF: 0.426 AC: 4483 AN: 10530

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.464 AC: 31538 AN: 67948

Other (OTH) AF: 0.444 AC: 936 AN: 2110

Alfa AF: 0.446 Hom.: 28645

Bravo AF: 0.401

Asia WGS AF: 0.354 AC: 1230 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.20
DANN	Benign	0.66
PhyloP100		-0.77
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: rs2160138; hg19: chr7-7755797;