rs7780564

chr7-7843692-A-Cchr7-7843692-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.157-33589A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.536 in 151,336 control chromosomes in the GnomAD database, including 21,915 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 0.54 (21915 hom., cov: 31)
• Consequence: UMAD1 NM_001302348.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.426

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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.576 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UMAD1	NM_001302348.2	c.157-33589A>C		intron_variant		ENST00000682710.1
UMAD1	NM_001302349.2	c.157-33589A>C		intron_variant
UMAD1	NM_001302350.2	c.52-33589A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UMAD1	ENST00000682710.1	c.157-33589A>C		intron_variant			NM_001302348.2	P1

Frequencies

GnomAD3 genomes AF: 0.536 AC: 81029 AN: 151216 Hom.: 21915 Cov.: 31

Gnomad AFR AF: 0.532

Gnomad AMI AF: 0.615

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.646

Gnomad EAS AF: 0.428

Gnomad SAS AF: 0.595

Gnomad FIN AF: 0.540

Gnomad MID AF: 0.641

Gnomad NFE AF: 0.550

Gnomad OTH AF: 0.567

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

GnomAD4 genome AF: 0.536 AC: 81055 AN: 151336 Hom.: 21915 Cov.: 31 AF XY: 0.533 AC XY: 39365 AN XY: 73924

Gnomad4 AFR AF: 0.531

Gnomad4 AMR AF: 0.462

Gnomad4 ASJ AF: 0.646

Gnomad4 EAS AF: 0.428

Gnomad4 SAS AF: 0.594

Gnomad4 FIN AF: 0.540

Gnomad4 NFE AF: 0.550

Gnomad4 OTH AF: 0.562

Alfa AF: 0.551 Hom.: 42811

Bravo AF: 0.531

Asia WGS AF: 0.501 AC: 1743 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.3
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7780564; hg19: chr7-7883323;