7-7898965-C-T

Variant names:

• chr7-7898965-C-T
• rs10486201
• ENST00000482067.3:c.157-68734C>T

Variant summary

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

The XR_007060205.1(LOC124901586):​n.963+8267G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0995 in 152,152 control chromosomes in the GnomAD database, including 1,015 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 0.099 (1015 hom., cov: 32)
• Consequence: LOC124901586 XR_007060205.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0610
• Publications: 6 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.134 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000482067.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UMAD1	ENST00000482067.3	TSL:5	c.157-68734C>T		intron	N/A	ENSP00000490046.1	A0A1B0GUC2
	ENSG00000283549	ENST00000469183.5	TSL:5	n.491+97222C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0996 AC: 15142 AN: 152034 Hom.: 1016 Cov.: 32

Gnomad AFR AF: 0.0212

Gnomad AMI AF: 0.0593

Gnomad AMR AF: 0.0988

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.0787

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.0995 AC: 15137 AN: 152152 Hom.: 1015 Cov.: 32 AF XY: 0.100 AC XY: 7451 AN XY: 74374

African (AFR) AF: 0.0211 AC: 877 AN: 41528

American (AMR) AF: 0.0986 AC: 1507 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.207 AC: 717 AN: 3464

East Asian (EAS) AF: 0.0785 AC: 407 AN: 5186

South Asian (SAS) AF: 0.102 AC: 492 AN: 4818

European-Finnish (FIN) AF: 0.146 AC: 1541 AN: 10566

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.136 AC: 9250 AN: 67998

Other (OTH) AF: 0.119 AC: 250 AN: 2108

Alfa AF: 0.117 Hom.: 2061

Bravo AF: 0.0934

Asia WGS AF: 0.0740 AC: 257 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.0
DANN	Benign	0.80
PhyloP100		0.061

Splicing

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

Other links and lift over

dbSNP: rs10486201; hg19: chr7-7938596;