rs10495886

Variant names:

• chr2-40861360-G-A
• rs10495886
• ENST00000753888.1:n.150-24032C>T

Your query was ambiguous. Multiple possible variants found:

• chr2-40861360-G-A
• chr2-40861360-G-C

Variant summary

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

The ENST00000753888.1(ENSG00000298207):​n.150-24032C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0382 in 152,170 control chromosomes in the GnomAD database, including 577 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 0.038 (577 hom., cov: 32)
• Consequence: ENSG00000298207 ENST00000753888.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.691
• Publications: 1 publications found

Genes affected

ENSG00000298207 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.262 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374497	XR_001739421.3	n.60-24032C>T		intron_variant	Intron 1 of 3
LOC105374497	XR_001739422.1	n.1509-24032C>T		intron_variant	Intron 1 of 3
LOC105374497	XR_001739423.1	n.60-24032C>T		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298207	ENST00000753888.1	n.150-24032C>T		intron_variant	Intron 2 of 4
ENSG00000298207	ENST00000753889.1	n.150-24032C>T		intron_variant	Intron 2 of 5
ENSG00000298207	ENST00000753890.1	n.246-24032C>T		intron_variant	Intron 3 of 6
ENSG00000298207	ENST00000753891.1	n.246-24032C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.0382 AC: 5806 AN: 152052 Hom.: 571 Cov.: 32

Gnomad AFR AF: 0.00823

Gnomad AMI AF: 0.0198

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.00979

Gnomad EAS AF: 0.273

Gnomad SAS AF: 0.0379

Gnomad FIN AF: 0.00858

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0118

Gnomad OTH AF: 0.0488

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

GnomAD4 genome AF: 0.0382 AC: 5811 AN: 152170 Hom.: 577 Cov.: 32 AF XY: 0.0425 AC XY: 3164 AN XY: 74402

African (AFR) AF: 0.00819 AC: 340 AN: 41534

American (AMR) AF: 0.185 AC: 2825 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.00979 AC: 34 AN: 3472

East Asian (EAS) AF: 0.273 AC: 1416 AN: 5178

South Asian (SAS) AF: 0.0373 AC: 180 AN: 4822

European-Finnish (FIN) AF: 0.00858 AC: 91 AN: 10612

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0118 AC: 804 AN: 67990

Other (OTH) AF: 0.0478 AC: 101 AN: 2112

Alfa AF: 0.00427 Hom.: 2

Bravo AF: 0.0550

Asia WGS AF: 0.138 AC: 479 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.73
DANN	Benign	0.39
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs10495886; hg19: chr2-41088500;