rs10496262

Variant names:

• chr2-81524000-C-A
• rs10496262
• ENST00000817540.1:n.373-24618C>A

Your query was ambiguous. Multiple possible variants found:

• chr2-81524000-C-A
• chr2-81524000-C-G

Variant summary

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

The NR_187691.1(LOC102724542):​n.368-24618C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 151,946 control chromosomes in the GnomAD database, including 1,325 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 0.12 (1325 hom., cov: 32)
• Consequence: LOC102724542 NR_187691.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.684
• Publications: 10 publications found

Genes affected

ENSG00000306384 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.167 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_187691.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC102724542	NR_187691.1		n.368-24618C>A		intron	N/A
	LOC102724542	NR_187692.1		n.368-24618C>A		intron	N/A
	LOC102724542	NR_187693.1		n.368-24618C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000306384	ENST00000817540.1		n.373-24618C>A		intron	N/A
	ENSG00000306384	ENST00000817541.1		n.371-24618C>A		intron	N/A
	ENSG00000306384	ENST00000817542.1		n.366-24618C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17711 AN: 151828 Hom.: 1325 Cov.: 32

Gnomad AFR AF: 0.0422

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.0796

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.00894

Gnomad SAS AF: 0.0458

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.0701

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.0997

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

GnomAD4 genome AF: 0.117 AC: 17709 AN: 151946 Hom.: 1325 Cov.: 32 AF XY: 0.113 AC XY: 8410 AN XY: 74252

African (AFR) AF: 0.0421 AC: 1747 AN: 41498

American (AMR) AF: 0.0795 AC: 1211 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.130 AC: 449 AN: 3464

East Asian (EAS) AF: 0.00896 AC: 46 AN: 5134

South Asian (SAS) AF: 0.0459 AC: 221 AN: 4820

European-Finnish (FIN) AF: 0.191 AC: 2020 AN: 10564

Middle Eastern (MID) AF: 0.0616 AC: 18 AN: 292

European-Non Finnish (NFE) AF: 0.170 AC: 11533 AN: 67914

Other (OTH) AF: 0.0987 AC: 208 AN: 2108

Alfa AF: 0.151 Hom.: 2947

Bravo AF: 0.107

Asia WGS AF: 0.0250 AC: 88 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.1
DANN	Benign	0.70
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs10496262; hg19: chr2-81751124;