rs13237260

Variant names:

• chr7-7739460-G-T
• rs13237260
• NM_001302348.2:c.83-62210G>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.83-62210G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.291 in 152,064 control chromosomes in the GnomAD database, including 7,363 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 0.29 (7363 hom., cov: 33)
• Consequence: UMAD1 NM_001302348.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0770
• Publications: 3 publications found

Genes affected

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

ENSG00000293038 (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 = 0.457 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UMAD1	NM_001302348.2	c.83-62210G>T		intron_variant	Intron 2 of 3	ENST00000682710.1	NP_001289277.1
UMAD1	NM_001302349.2	c.83-62210G>T		intron_variant	Intron 2 of 3		NP_001289278.1
UMAD1	NM_001302350.2	c.-23-62210G>T		intron_variant	Intron 3 of 4		NP_001289279.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UMAD1	ENST00000682710.1	c.83-62210G>T		intron_variant	Intron 2 of 3		NM_001302348.2	ENSP00000507605.1

Frequencies

GnomAD3 genomes AF: 0.291 AC: 44268 AN: 151944 Hom.: 7348 Cov.: 33

Gnomad AFR AF: 0.463

Gnomad AMI AF: 0.444

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.228

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.291 AC: 44321 AN: 152064 Hom.: 7363 Cov.: 33 AF XY: 0.287 AC XY: 21336 AN XY: 74330

African (AFR) AF: 0.463 AC: 19186 AN: 41464

American (AMR) AF: 0.206 AC: 3153 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.236 AC: 820 AN: 3468

East Asian (EAS) AF: 0.222 AC: 1145 AN: 5162

South Asian (SAS) AF: 0.272 AC: 1313 AN: 4824

European-Finnish (FIN) AF: 0.200 AC: 2110 AN: 10562

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.228 AC: 15487 AN: 67974

Other (OTH) AF: 0.286 AC: 605 AN: 2114

Alfa AF: 0.244 Hom.: 6413

Bravo AF: 0.301

Asia WGS AF: 0.310 AC: 1076 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.0
DANN	Benign	0.64
PhyloP100		0.077

Splicing

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

Other links and lift over

dbSNP: rs13237260; hg19: chr7-7779091;