NM_001302348.2:c.82+42407C>A

Variant names:

• chr7-7715860-C-A
• rs7456324
• NM_001302348.2:c.82+42407C>A

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+42407C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.083 in 152,120 control chromosomes in the GnomAD database, including 619 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 0.083 (619 hom., cov: 32)
• Consequence: UMAD1 NM_001302348.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.580
• 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=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0959 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+42407C>A		intron	N/A	NP_001289277.1
	RPA3	NM_002947.5	MANE Select	c.-1079-634G>T		intron	N/A	NP_002938.1
	UMAD1	NM_001302349.2		c.82+42407C>A		intron	N/A	NP_001289278.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UMAD1	ENST00000682710.1	MANE Select	c.82+42407C>A		intron	N/A	ENSP00000507605.1
	RPA3	ENST00000223129.8	TSL:1 MANE Select	c.-1079-634G>T		intron	N/A	ENSP00000223129.4
	UMAD1	ENST00000949980.1		c.189+39652C>A		intron	N/A	ENSP00000620039.1

Frequencies

GnomAD3 genomes AF: 0.0829 AC: 12607 AN: 152002 Hom.: 617 Cov.: 32

Gnomad AFR AF: 0.0397

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.0951

Gnomad ASJ AF: 0.0735

Gnomad EAS AF: 0.0254

Gnomad SAS AF: 0.0883

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0978

Gnomad OTH AF: 0.0771

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

GnomAD4 genome AF: 0.0830 AC: 12624 AN: 152120 Hom.: 619 Cov.: 32 AF XY: 0.0863 AC XY: 6419 AN XY: 74348

African (AFR) AF: 0.0398 AC: 1654 AN: 41540

American (AMR) AF: 0.0952 AC: 1455 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0735 AC: 255 AN: 3468

East Asian (EAS) AF: 0.0251 AC: 130 AN: 5188

South Asian (SAS) AF: 0.0888 AC: 428 AN: 4818

European-Finnish (FIN) AF: 0.157 AC: 1653 AN: 10532

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0979 AC: 6651 AN: 67970

Other (OTH) AF: 0.0782 AC: 165 AN: 2110

Alfa AF: 0.0790 Hom.: 282

Bravo AF: 0.0762

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.2
DANN	Benign	0.22
PhyloP100		0.58
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: rs7456324; hg19: chr7-7755491;