chr10-93751506-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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000793614.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000303320	ENST00000793614.1		n.208-1522G>A		intron	N/A
	ENSG00000303320	ENST00000793616.1		n.244-1522G>A		intron	N/A
	ENSG00000303320	ENST00000793617.1		n.757+4031G>A		intron	N/A

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 v4.9

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;