rs7812102

Positions:

• chr7-7867029-G-A

Variant summary

Our verdict is Benign. Variant got -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

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=-0.9).
• 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/exons	MANE	Protein	UniProt
UMAD1	NM_001302348.2	c.157-10252G>A		intron_variant		ENST00000682710.1	NP_001289277.1
UMAD1	NM_001302349.2	c.157-10252G>A		intron_variant			NP_001289278.1
UMAD1	NM_001302350.2	c.52-10252G>A		intron_variant			NP_001289279.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UMAD1	ENST00000682710.1	c.157-10252G>A		intron_variant			NM_001302348.2	ENSP00000507605	P1

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

Gnomad4 AFR AF: 0.425

Gnomad4 AMR AF: 0.229

Gnomad4 ASJ AF: 0.103

Gnomad4 EAS AF: 0.141

Gnomad4 SAS AF: 0.228

Gnomad4 FIN AF: 0.0509

Gnomad4 NFE AF: 0.0996

Gnomad4 OTH AF: 0.177

Alfa AF: 0.132 Hom.: 1019

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7812102; hg19: chr7-7906660;