rs10486192

Positions:

• chr7-7842503-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001302348.2(UMAD1):​c.157-34778G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0337 in 151,746 control chromosomes in the GnomAD database, including 232 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 0.034 (232 hom., cov: 31)
• Consequence: UMAD1 NM_001302348.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.272

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.202 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UMAD1	NM_001302348.2	c.157-34778G>C		intron_variant		ENST00000682710.1	NP_001289277.1
UMAD1	NM_001302349.2	c.157-34778G>C		intron_variant			NP_001289278.1
UMAD1	NM_001302350.2	c.52-34778G>C		intron_variant			NP_001289279.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UMAD1	ENST00000682710.1	c.157-34778G>C		intron_variant			NM_001302348.2	ENSP00000507605	P1

Frequencies

GnomAD3 genomes AF: 0.0338 AC: 5125 AN: 151630 Hom.: 234 Cov.: 31

Gnomad AFR AF: 0.0368

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.0377

Gnomad ASJ AF: 0.0300

Gnomad EAS AF: 0.214

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.00887

Gnomad MID AF: 0.0669

Gnomad NFE AF: 0.0146

Gnomad OTH AF: 0.0284

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

GnomAD4 genome AF: 0.0337 AC: 5115 AN: 151746 Hom.: 232 Cov.: 31 AF XY: 0.0368 AC XY: 2729 AN XY: 74106

Gnomad4 AFR AF: 0.0368

Gnomad4 AMR AF: 0.0376

Gnomad4 ASJ AF: 0.0300

Gnomad4 EAS AF: 0.213

Gnomad4 SAS AF: 0.128

Gnomad4 FIN AF: 0.00887

Gnomad4 NFE AF: 0.0146

Gnomad4 OTH AF: 0.0281

Alfa AF: 0.0219 Hom.: 7

Bravo AF: 0.0344

Asia WGS AF: 0.179 AC: 618 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	10
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10486192; hg19: chr7-7882134;