rs2068637

Positions:

• chr7-7740716-C-T

Variant summary

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

The NM_001302348.2(UMAD1):​c.83-60954C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.205 in 152,182 control chromosomes in the GnomAD database, including 3,617 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 0.21 (3617 hom., cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: UMAD1 NM_001302348.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.227

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.315 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UMAD1	NM_001302348.2	c.83-60954C>T		intron_variant		ENST00000682710.1
UMAD1	NM_001302349.2	c.83-60954C>T		intron_variant
UMAD1	NM_001302350.2	c.-23-60954C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UMAD1	ENST00000682710.1	c.83-60954C>T		intron_variant			NM_001302348.2	P1
	ENST00000418534.3	n.600+1259G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.205 AC: 31187 AN: 152064 Hom.: 3619 Cov.: 33

Gnomad AFR AF: 0.320

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.206

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.205 AC: 31201 AN: 152182 Hom.: 3617 Cov.: 33 AF XY: 0.200 AC XY: 14883 AN XY: 74422

Gnomad4 AFR AF: 0.320

Gnomad4 AMR AF: 0.155

Gnomad4 ASJ AF: 0.168

Gnomad4 EAS AF: 0.206

Gnomad4 SAS AF: 0.158

Gnomad4 FIN AF: 0.131

Gnomad4 NFE AF: 0.163

Gnomad4 OTH AF: 0.206

Alfa AF: 0.172 Hom.: 1117

Bravo AF: 0.214

Asia WGS AF: 0.212 AC: 734 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.6
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2068637; hg19: chr7-7780347;