rs2243492

Variant names:

• chr10-43353910-T-C
• rs2243492
• ENST00000765039.1:n.111-3394A>G

Your query was ambiguous. Multiple possible variants found:

• chr10-43353910-T-C
• chr10-43353910-T-G

Variant summary

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

The ENST00000765039.1(ENSG00000285712):​n.111-3394A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.779 in 152,130 control chromosomes in the GnomAD database, including 47,635 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 0.78 (47635 hom., cov: 33)
• Consequence: ENSG00000285712 ENST00000765039.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0850
• Publications: 6 publications found

Genes affected

ENSG00000285712 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.886 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000765039.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285712	ENST00000765039.1		n.111-3394A>G		intron	N/A
	ENSG00000285712	ENST00000765040.1		n.107-2770A>G		intron	N/A
	ENSG00000285712	ENST00000765041.1		n.96-3394A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.780 AC: 118517 AN: 152012 Hom.: 47621 Cov.: 33

Gnomad AFR AF: 0.580

Gnomad AMI AF: 0.930

Gnomad AMR AF: 0.823

Gnomad ASJ AF: 0.875

Gnomad EAS AF: 0.614

Gnomad SAS AF: 0.745

Gnomad FIN AF: 0.819

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.892

Gnomad OTH AF: 0.816

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

GnomAD4 genome AF: 0.779 AC: 118568 AN: 152130 Hom.: 47635 Cov.: 33 AF XY: 0.774 AC XY: 57534 AN XY: 74352

African (AFR) AF: 0.580 AC: 24050 AN: 41480

American (AMR) AF: 0.822 AC: 12555 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.875 AC: 3037 AN: 3472

East Asian (EAS) AF: 0.613 AC: 3171 AN: 5172

South Asian (SAS) AF: 0.746 AC: 3596 AN: 4820

European-Finnish (FIN) AF: 0.819 AC: 8654 AN: 10572

Middle Eastern (MID) AF: 0.854 AC: 251 AN: 294

European-Non Finnish (NFE) AF: 0.892 AC: 60680 AN: 68022

Other (OTH) AF: 0.816 AC: 1726 AN: 2116

Alfa AF: 0.851 Hom.: 44076

Bravo AF: 0.771

Asia WGS AF: 0.663 AC: 2307 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	8.1
DANN	Benign	0.37
PhyloP100		0.085

Splicing

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

Other links and lift over

dbSNP: rs2243492; hg19: chr10-43849358;