10-93751506-C-T

Variant names:

• chr10-93751506-C-T
• rs2095890
• ENST00000793614.1:n.208-1522G>A

Variant summary

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

The ENST00000793614.1(ENSG00000303320):​n.208-1522G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.243 in 151,950 control chromosomes in the GnomAD database, including 5,612 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 0.24 (5612 hom., cov: 31)
• Consequence: ENSG00000303320 ENST00000793614.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.568
• Publications: 0 publications found

Genes affected

ENSG00000303320 (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 (AFR) allele frequency at 95% confidence interval = 0.415 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927013	XR_246160.5	n.238-1522G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000303320	ENST00000793614.1	n.208-1522G>A		intron_variant	Intron 1 of 3
ENSG00000303320	ENST00000793616.1	n.244-1522G>A		intron_variant	Intron 1 of 2
ENSG00000303320	ENST00000793617.1	n.757+4031G>A		intron_variant	Intron 2 of 2
ENSG00000303320	ENST00000793618.1	n.619-5399G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36914 AN: 151832 Hom.: 5599 Cov.: 31

Gnomad AFR AF: 0.421

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.0969

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.243 AC: 36958 AN: 151950 Hom.: 5612 Cov.: 31 AF XY: 0.233 AC XY: 17329 AN XY: 74264

African (AFR) AF: 0.421 AC: 17400 AN: 41360

American (AMR) AF: 0.184 AC: 2812 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.282 AC: 978 AN: 3468

East Asian (EAS) AF: 0.0969 AC: 500 AN: 5158

South Asian (SAS) AF: 0.121 AC: 585 AN: 4816

European-Finnish (FIN) AF: 0.119 AC: 1263 AN: 10570

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.185 AC: 12590 AN: 67988

Other (OTH) AF: 0.255 AC: 537 AN: 2108

Alfa AF: 0.0972 Hom.: 164

Bravo AF: 0.258

Asia WGS AF: 0.120 AC: 421 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.3
DANN	Benign	0.51
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs2095890; hg19: chr10-95511263;