rs17136953

chr7-7735884-A-G

Variant summary

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

The NM_001302348.2(UMAD1):c.82+62431A>G 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 152,210 control chromosomes in the GnomAD database, including 7,761 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 (7759 hom., cov: 32)
  • Exomes 𝑓: 0.39 (2 hom.)
• Consequence: UMAD1 NM_001302348.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.443

Genes affected

UMAD1 (HGNC:48955): (UBAP1-MVB12-associated (UMA) domain containing 1)

(HGNC:):

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 (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+62431A>G		intron_variant		ENST00000682710.1
UMAD1	NM_001302349.2	c.82+62431A>G		intron_variant
UMAD1	NM_001302350.2	c.-24+59676A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UMAD1	ENST00000682710.1	c.82+62431A>G		intron_variant			NM_001302348.2	P1
	ENST00000604734.1	n.968T>C		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.297 AC: 45163 AN: 152074 Hom.: 7741 Cov.: 32

Gnomad AFR AF: 0.482

Gnomad AMI AF: 0.446

Gnomad AMR AF: 0.208

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.221

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.199

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.228

Gnomad OTH AF: 0.290

GnomAD4 exome AF: 0.389 AC: 7 AN: 18 Hom.: 2 Cov.: 0 AF XY: 0.500 AC XY: 5 AN XY: 10

Gnomad4 FIN exome AF: 0.125

Gnomad4 NFE exome AF: 0.600

GnomAD4 genome AF: 0.297 AC: 45221 AN: 152192 Hom.: 7759 Cov.: 32 AF XY: 0.293 AC XY: 21775 AN XY: 74414

Gnomad4 AFR AF: 0.482

Gnomad4 AMR AF: 0.208

Gnomad4 ASJ AF: 0.236

Gnomad4 EAS AF: 0.222

Gnomad4 SAS AF: 0.273

Gnomad4 FIN AF: 0.199

Gnomad4 NFE AF: 0.228

Gnomad4 OTH AF: 0.291

Alfa AF: 0.258 Hom.: 750

Bravo AF: 0.307

Asia WGS AF: 0.313 AC: 1087 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.7
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17136953; hg19: chr7-7775515;