rs10486192

Variant names:

• chr7-7842503-G-C
• rs10486192
• NM_001302348.2:c.157-34778G>C

Your query was ambiguous. Multiple possible variants found:

• chr7-7842503-G-C
• chr7-7842503-G-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.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
• Publications: 1 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=-0.92).
• 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 rank	MANE	Protein	UniProt
UMAD1	NM_001302348.2	c.157-34778G>C		intron_variant	Intron 3 of 3	ENST00000682710.1	NP_001289277.1
UMAD1	NM_001302349.2	c.157-34778G>C		intron_variant	Intron 3 of 3		NP_001289278.1
UMAD1	NM_001302350.2	c.52-34778G>C		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.157-34778G>C		intron_variant	Intron 3 of 3		NM_001302348.2	ENSP00000507605.1

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

African (AFR) AF: 0.0368 AC: 1521 AN: 41370

American (AMR) AF: 0.0376 AC: 572 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.0300 AC: 104 AN: 3468

East Asian (EAS) AF: 0.213 AC: 1099 AN: 5168

South Asian (SAS) AF: 0.128 AC: 615 AN: 4790

European-Finnish (FIN) AF: 0.00887 AC: 93 AN: 10480

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0146 AC: 990 AN: 67950

Other (OTH) AF: 0.0281 AC: 59 AN: 2102

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
PhyloP100		0.27
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: rs10486192; hg19: chr7-7882134;