NM_001302348.2:c.157-10252G>A

Variant names:

• chr7-7867029-G-A
• rs7812102
• NM_001302348.2:c.157-10252G>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.157-10252G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.204 in 151,840 control chromosomes in the GnomAD database, including 4,807 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 (4807 hom., cov: 31)
• Consequence: UMAD1 NM_001302348.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.650
• Publications: 2 publications found

Genes affected

UMAD1 (HGNC:48955): (UBAP1-MVB12-associated (UMA) domain containing 1)

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 (AFR) allele frequency at 95% confidence interval = 0.419 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UMAD1	NM_001302348.2	c.157-10252G>A		intron_variant	Intron 3 of 3	ENST00000682710.1	NP_001289277.1
UMAD1	NM_001302349.2	c.157-10252G>A		intron_variant	Intron 3 of 3		NP_001289278.1
UMAD1	NM_001302350.2	c.52-10252G>A		intron_variant	Intron 4 of 4		NP_001289279.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UMAD1	ENST00000682710.1	c.157-10252G>A		intron_variant	Intron 3 of 3		NM_001302348.2	ENSP00000507605.1

Frequencies

GnomAD3 genomes AF: 0.204 AC: 30966 AN: 151722 Hom.: 4797 Cov.: 31

Gnomad AFR AF: 0.424

Gnomad AMI AF: 0.0639

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.0509

Gnomad MID AF: 0.178

Gnomad NFE AF: 0.0996

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.204 AC: 31023 AN: 151840 Hom.: 4807 Cov.: 31 AF XY: 0.203 AC XY: 15065 AN XY: 74220

African (AFR) AF: 0.425 AC: 17554 AN: 41344

American (AMR) AF: 0.229 AC: 3495 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 356 AN: 3470

East Asian (EAS) AF: 0.141 AC: 723 AN: 5144

South Asian (SAS) AF: 0.228 AC: 1099 AN: 4814

European-Finnish (FIN) AF: 0.0509 AC: 538 AN: 10564

Middle Eastern (MID) AF: 0.192 AC: 56 AN: 292

European-Non Finnish (NFE) AF: 0.0996 AC: 6771 AN: 67952

Other (OTH) AF: 0.177 AC: 373 AN: 2108

Alfa AF: 0.133 Hom.: 1151

Bravo AF: 0.227

Asia WGS AF: 0.222 AC: 770 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.5
DANN	Benign	0.79
PhyloP100		-0.65
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7812102; hg19: chr7-7906660;