rs12702661

chr7-7825120-A-Gchr7-7825120-A-T

Variant summary

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

The NM_001302348.2(UMAD1):c.156+23377A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.792 in 151,984 control chromosomes in the GnomAD database, including 47,725 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 0.79 (47725 hom., cov: 30)
• Consequence: UMAD1 NM_001302348.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.109

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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.83 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UMAD1	NM_001302348.2	c.156+23377A>G		intron_variant		ENST00000682710.1
UMAD1	NM_001302349.2	c.156+23377A>G		intron_variant
UMAD1	NM_001302350.2	c.51+23377A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UMAD1	ENST00000682710.1	c.156+23377A>G		intron_variant			NM_001302348.2	P1

Frequencies

GnomAD3 genomes AF: 0.792 AC: 120261 AN: 151866 Hom.: 47690 Cov.: 30

Gnomad AFR AF: 0.837

Gnomad AMI AF: 0.795

Gnomad AMR AF: 0.749

Gnomad ASJ AF: 0.767

Gnomad EAS AF: 0.761

Gnomad SAS AF: 0.807

Gnomad FIN AF: 0.815

Gnomad MID AF: 0.777

Gnomad NFE AF: 0.774

Gnomad OTH AF: 0.766

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

GnomAD4 genome AF: 0.792 AC: 120349 AN: 151984 Hom.: 47725 Cov.: 30 AF XY: 0.794 AC XY: 59001 AN XY: 74266

Gnomad4 AFR AF: 0.837

Gnomad4 AMR AF: 0.749

Gnomad4 ASJ AF: 0.767

Gnomad4 EAS AF: 0.761

Gnomad4 SAS AF: 0.808

Gnomad4 FIN AF: 0.815

Gnomad4 NFE AF: 0.774

Gnomad4 OTH AF: 0.761

Alfa AF: 0.771 Hom.: 92323

Bravo AF: 0.787

Asia WGS AF: 0.783 AC: 2728 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	3.9
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: rs12702661; hg19: chr7-7864751;