rs10259199

Positions:

• chr7-7809281-T-C
• chr7-7809281-T-G

Variant summary

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

The NM_001302348.2(UMAD1):​c.156+7538T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 151,856 control chromosomes in the GnomAD database, including 2,535 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 0.17 (2535 hom., cov: 32)
• Consequence: UMAD1 NM_001302348.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.790

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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.249 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UMAD1	NM_001302348.2	c.156+7538T>C		intron_variant		ENST00000682710.1
UMAD1	NM_001302349.2	c.156+7538T>C		intron_variant
UMAD1	NM_001302350.2	c.51+7538T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UMAD1	ENST00000682710.1	c.156+7538T>C		intron_variant			NM_001302348.2	P1

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26112 AN: 151738 Hom.: 2532 Cov.: 32

Gnomad AFR AF: 0.253

Gnomad AMI AF: 0.304

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.0825

Gnomad SAS AF: 0.0704

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.172 AC: 26127 AN: 151856 Hom.: 2535 Cov.: 32 AF XY: 0.174 AC XY: 12940 AN XY: 74244

Gnomad4 AFR AF: 0.253

Gnomad4 AMR AF: 0.136

Gnomad4 ASJ AF: 0.221

Gnomad4 EAS AF: 0.0825

Gnomad4 SAS AF: 0.0702

Gnomad4 FIN AF: 0.218

Gnomad4 NFE AF: 0.133

Gnomad4 OTH AF: 0.168

Alfa AF: 0.137 Hom.: 2074

Bravo AF: 0.170

Asia WGS AF: 0.0990 AC: 344 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.90
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10259199; hg19: chr7-7848912;