rs10495355

Variant names:

• chr1-234882459-C-T
• rs10495355
• ENST00000651370.2:n.234+50010G>A

Variant summary

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

The ENST00000651370.2(ENSG00000286263):​n.234+50010G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.238 in 152,072 control chromosomes in the GnomAD database, including 5,018 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 (5018 hom., cov: 32)
• Consequence: ENSG00000286263 ENST00000651370.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.455
• Publications: 2 publications found

Genes affected

ENSG00000286263 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.518 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000651370.2. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286263	ENST00000651370.2		n.234+50010G>A		intron	N/A
	ENSG00000286263	ENST00000850398.1		n.309+30283G>A		intron	N/A
	ENSG00000286263	ENST00000850399.1		n.281+30283G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.238 AC: 36168 AN: 151954 Hom.: 5009 Cov.: 32

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.0998

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.533

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.265

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

GnomAD4 genome AF: 0.238 AC: 36206 AN: 152072 Hom.: 5018 Cov.: 32 AF XY: 0.244 AC XY: 18142 AN XY: 74344

African (AFR) AF: 0.273 AC: 11301 AN: 41448

American (AMR) AF: 0.373 AC: 5689 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.256 AC: 889 AN: 3472

East Asian (EAS) AF: 0.534 AC: 2762 AN: 5168

South Asian (SAS) AF: 0.319 AC: 1538 AN: 4826

European-Finnish (FIN) AF: 0.150 AC: 1587 AN: 10584

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.172 AC: 11706 AN: 67986

Other (OTH) AF: 0.268 AC: 566 AN: 2112

Alfa AF: 0.202 Hom.: 5748

Bravo AF: 0.258

Asia WGS AF: 0.434 AC: 1511 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	3.7
DANN	Benign	0.88
PhyloP100		0.46

Splicing

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

Other links and lift over

dbSNP: rs10495355; hg19: chr1-235018206;