rs10952069

Positions:

• chr7-7735053-C-T

Variant summary

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

The NM_001302348.2(UMAD1):​c.82+61600C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.297 in 151,842 control chromosomes in the GnomAD database, including 7,736 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 0.30 (7736 hom., cov: 32)
• Consequence: UMAD1 NM_001302348.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0650

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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.477 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UMAD1	NM_001302348.2	c.82+61600C>T		intron_variant		ENST00000682710.1
UMAD1	NM_001302349.2	c.82+61600C>T		intron_variant
UMAD1	NM_001302350.2	c.-24+58845C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UMAD1	ENST00000682710.1	c.82+61600C>T		intron_variant			NM_001302348.2	P1

Frequencies

GnomAD3 genomes AF: 0.297 AC: 45076 AN: 151724 Hom.: 7718 Cov.: 32

Gnomad AFR AF: 0.483

Gnomad AMI AF: 0.446

Gnomad AMR AF: 0.208

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.221

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.228

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.297 AC: 45134 AN: 151842 Hom.: 7736 Cov.: 32 AF XY: 0.293 AC XY: 21742 AN XY: 74214

Gnomad4 AFR AF: 0.483

Gnomad4 AMR AF: 0.207

Gnomad4 ASJ AF: 0.235

Gnomad4 EAS AF: 0.222

Gnomad4 SAS AF: 0.273

Gnomad4 FIN AF: 0.201

Gnomad4 NFE AF: 0.228

Gnomad4 OTH AF: 0.292

Alfa AF: 0.242 Hom.: 5532

Bravo AF: 0.306

Asia WGS AF: 0.313 AC: 1084 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.1
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10952069; hg19: chr7-7774684;