rs10952069

Variant names:

• chr7-7735053-C-T
• rs10952069
• NM_001302348.2:c.82+61600C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001302348.2(UMAD1):​c.82+61600C>T 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 151,842 control chromosomes in the GnomAD database, including 7,736 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 (7736 hom., cov: 32)
• Consequence: UMAD1 NM_001302348.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0650
• Publications: 4 publications found

Genes affected

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

ENSG00000283549 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.477 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001302348.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UMAD1	NM_001302348.2	MANE Select	c.82+61600C>T		intron	N/A	NP_001289277.1
	UMAD1	NM_001302349.2		c.82+61600C>T		intron	N/A	NP_001289278.1
	UMAD1	NM_001302350.2		c.-24+58845C>T		intron	N/A	NP_001289279.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UMAD1	ENST00000682710.1	MANE Select	c.82+61600C>T		intron	N/A	ENSP00000507605.1
	UMAD1	ENST00000636849.1	TSL:5	c.82+61600C>T		intron	N/A	ENSP00000489648.1
	UMAD1	ENST00000482067.3	TSL:5	c.82+61600C>T		intron	N/A	ENSP00000490046.1

Frequencies

GnomAD3 genomes AF: 0.297 AC: 45076 AN: 151724 Hom.: 7718 Cov.: 32

Gnomad AFR AF: 0.483

Gnomad AMI AF: 0.446

Gnomad AMR AF: 0.208

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.221

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.228

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.297 AC: 45134 AN: 151842 Hom.: 7736 Cov.: 32 AF XY: 0.293 AC XY: 21742 AN XY: 74214

African (AFR) AF: 0.483 AC: 19972 AN: 41378

American (AMR) AF: 0.207 AC: 3165 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.235 AC: 815 AN: 3470

East Asian (EAS) AF: 0.222 AC: 1142 AN: 5152

South Asian (SAS) AF: 0.273 AC: 1316 AN: 4822

European-Finnish (FIN) AF: 0.201 AC: 2109 AN: 10502

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.228 AC: 15496 AN: 67948

Other (OTH) AF: 0.292 AC: 616 AN: 2112

Alfa AF: 0.262 Hom.: 9134

Bravo AF: 0.306

Asia WGS AF: 0.313 AC: 1084 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.1
DANN	Benign	0.29
PhyloP100		0.065

Splicing

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

Other links and lift over

dbSNP: rs10952069; hg19: chr7-7774684;