rs11687663

Variant names:

• chr2-150901931-T-C
• rs11687663
• ENST00000812494.1:n.382+13041A>G

Variant summary

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

The ENST00000812494.1(ENSG00000222031):​n.382+13041A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.321 in 151,954 control chromosomes in the GnomAD database, including 8,725 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 0.32 (8725 hom., cov: 31)
• Consequence: ENSG00000222031 ENST00000812494.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.588
• Publications: 2 publications found

Genes affected

ENSG00000222031 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.43 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000812494.1. 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
	ENSG00000222031	ENST00000812494.1		n.382+13041A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.321 AC: 48747 AN: 151836 Hom.: 8718 Cov.: 31

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.417

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.353

Gnomad EAS AF: 0.0885

Gnomad SAS AF: 0.447

Gnomad FIN AF: 0.436

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.403

Gnomad OTH AF: 0.324

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

GnomAD4 genome AF: 0.321 AC: 48765 AN: 151954 Hom.: 8725 Cov.: 31 AF XY: 0.322 AC XY: 23917 AN XY: 74258

African (AFR) AF: 0.187 AC: 7740 AN: 41470

American (AMR) AF: 0.268 AC: 4095 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.353 AC: 1225 AN: 3472

East Asian (EAS) AF: 0.0883 AC: 456 AN: 5164

South Asian (SAS) AF: 0.445 AC: 2141 AN: 4808

European-Finnish (FIN) AF: 0.436 AC: 4600 AN: 10552

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.403 AC: 27355 AN: 67914

Other (OTH) AF: 0.324 AC: 682 AN: 2102

Alfa AF: 0.374 Hom.: 8140

Bravo AF: 0.298

Asia WGS AF: 0.279 AC: 971 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.6
DANN	Benign	0.46
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs11687663; hg19: chr2-151758445;