rs2348763

chr7-7858084-A-Cchr7-7858084-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.157-19197A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.25 in 152,138 control chromosomes in the GnomAD database, including 5,795 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 0.25 (5795 hom., cov: 32)
• Consequence: UMAD1 NM_001302348.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.338

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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.33 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UMAD1	NM_001302348.2	c.157-19197A>C		intron_variant		ENST00000682710.1
UMAD1	NM_001302349.2	c.157-19197A>C		intron_variant
UMAD1	NM_001302350.2	c.52-19197A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UMAD1	ENST00000682710.1	c.157-19197A>C		intron_variant			NM_001302348.2	P1

Frequencies

GnomAD3 genomes AF: 0.251 AC: 38113 AN: 152020 Hom.: 5797 Cov.: 32

Gnomad AFR AF: 0.0764

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.284

Gnomad ASJ AF: 0.454

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.250 AC: 38107 AN: 152138 Hom.: 5795 Cov.: 32 AF XY: 0.249 AC XY: 18510 AN XY: 74370

Gnomad4 AFR AF: 0.0762

Gnomad4 AMR AF: 0.284

Gnomad4 ASJ AF: 0.454

Gnomad4 EAS AF: 0.194

Gnomad4 SAS AF: 0.310

Gnomad4 FIN AF: 0.283

Gnomad4 NFE AF: 0.333

Gnomad4 OTH AF: 0.276

Alfa AF: 0.312 Hom.: 3684

Bravo AF: 0.243

Asia WGS AF: 0.237 AC: 824 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	6.8
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2348763; hg19: chr7-7897715;