2-236894765-C-G

Variant names:

• chr2-236894765-C-G
• rs10192201
• ENST00000804689.1:n.87-17199C>G

Variant summary

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

The ENST00000804689.1(ENSG00000304566):​n.87-17199C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.611 in 151,924 control chromosomes in the GnomAD database, including 29,491 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 0.61 (29491 hom., cov: 32)
• Consequence: ENSG00000304566 ENST00000804689.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 1 publications found

Genes affected

ENSG00000304566 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.803 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000804689.1. 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
	ENSG00000304566	ENST00000804689.1		n.87-17199C>G		intron	N/A
	ENSG00000304566	ENST00000804690.1		n.232-171C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.611 AC: 92709 AN: 151806 Hom.: 29442 Cov.: 32

Gnomad AFR AF: 0.761

Gnomad AMI AF: 0.668

Gnomad AMR AF: 0.645

Gnomad ASJ AF: 0.602

Gnomad EAS AF: 0.824

Gnomad SAS AF: 0.715

Gnomad FIN AF: 0.536

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.500

Gnomad OTH AF: 0.596

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

GnomAD4 genome AF: 0.611 AC: 92814 AN: 151924 Hom.: 29491 Cov.: 32 AF XY: 0.617 AC XY: 45809 AN XY: 74230

African (AFR) AF: 0.761 AC: 31535 AN: 41454

American (AMR) AF: 0.645 AC: 9842 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.602 AC: 2089 AN: 3468

East Asian (EAS) AF: 0.824 AC: 4262 AN: 5174

South Asian (SAS) AF: 0.715 AC: 3444 AN: 4814

European-Finnish (FIN) AF: 0.536 AC: 5646 AN: 10524

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.500 AC: 33961 AN: 67908

Other (OTH) AF: 0.596 AC: 1256 AN: 2108

Alfa AF: 0.403 Hom.: 1014

Bravo AF: 0.621

Asia WGS AF: 0.748 AC: 2600 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.23
DANN	Benign	0.40
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs10192201; hg19: chr2-237803408;