chr7-7716166-T-C

Position:

• chr7-7716166-T-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UMAD1	NM_001302348.2	c.82+42713T>C		intron_variant		ENST00000682710.1	NP_001289277.1
RPA3	NM_002947.5	c.-1079-940A>G		intron_variant		ENST00000223129.8	NP_002938.1
UMAD1	NM_001302349.2	c.82+42713T>C		intron_variant			NP_001289278.1
UMAD1	NM_001302350.2	c.-24+39958T>C		intron_variant			NP_001289279.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UMAD1	ENST00000682710.1	c.82+42713T>C		intron_variant			NM_001302348.2	ENSP00000507605.1
RPA3	ENST00000223129.8	c.-1079-940A>G		intron_variant		1	NM_002947.5	ENSP00000223129.4

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

Gnomad4 AFR AF: 0.333

Gnomad4 AMR AF: 0.386

Gnomad4 ASJ AF: 0.517

Gnomad4 EAS AF: 0.195

Gnomad4 SAS AF: 0.415

Gnomad4 FIN AF: 0.426

Gnomad4 NFE AF: 0.464

Gnomad4 OTH AF: 0.444

Alfa AF: 0.452 Hom.: 21280

Bravo AF: 0.401

Asia WGS AF: 0.354 AC: 1230 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.20
DANN	Benign	0.66

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

Publications

LitVar

Other links and lift over

dbSNP: rs2160138; hg19: chr7-7755797;