rs10495886

Variant names:

• chr2-40861360-G-A
• rs10495886
• XR_001739421.3:n.60-24032C>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 XR_939994.2(LOC105374497):​n.60-24032C>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: LOC105374497 XR_939994.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.691

Genes affected

LOC105374497 (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

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

Gnomad4 AFR AF: 0.00819 AC: 0.00818606 AN: 0.00818606

Gnomad4 AMR AF: 0.185 AC: 0.185295 AN: 0.185295

Gnomad4 ASJ AF: 0.00979 AC: 0.00979263 AN: 0.00979263

Gnomad4 EAS AF: 0.273 AC: 0.273465 AN: 0.273465

Gnomad4 SAS AF: 0.0373 AC: 0.0373289 AN: 0.0373289

Gnomad4 FIN AF: 0.00858 AC: 0.0085752 AN: 0.0085752

Gnomad4 NFE AF: 0.0118 AC: 0.0118253 AN: 0.0118253

Gnomad4 OTH AF: 0.0478 AC: 0.047822 AN: 0.047822

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10495886; hg19: chr2-41088500;