rs2698530

Variant names:

• chr2-64276761-A-C
• rs2698530
• ENST00000684810.1:n.339+2714A>C

Your query was ambiguous. Multiple possible variants found:

• chr2-64276761-A-C
• chr2-64276761-A-G

Variant summary

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

The ENST00000684810.1(ENSG00000293670):​n.339+2714A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.238 in 152,096 control chromosomes in the GnomAD database, including 4,929 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 0.24 (4929 hom., cov: 32)
• Consequence: ENSG00000293670 ENST00000684810.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.31
• Publications: 13 publications found

Genes affected

ENSG00000293670 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.609 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000684810.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000293670	ENST00000684810.1		n.339+2714A>C		intron	N/A
	ENSG00000293670	ENST00000686684.1		n.266+2714A>C		intron	N/A
	ENSG00000293670	ENST00000689610.1		n.245+2714A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.238 AC: 36171 AN: 151978 Hom.: 4926 Cov.: 32

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.627

Gnomad SAS AF: 0.415

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.251

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

GnomAD4 genome AF: 0.238 AC: 36195 AN: 152096 Hom.: 4929 Cov.: 32 AF XY: 0.242 AC XY: 17965 AN XY: 74360

African (AFR) AF: 0.150 AC: 6216 AN: 41494

American (AMR) AF: 0.304 AC: 4642 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.262 AC: 908 AN: 3470

East Asian (EAS) AF: 0.627 AC: 3246 AN: 5174

South Asian (SAS) AF: 0.414 AC: 1991 AN: 4810

European-Finnish (FIN) AF: 0.217 AC: 2298 AN: 10582

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.237 AC: 16116 AN: 67956

Other (OTH) AF: 0.258 AC: 546 AN: 2114

Alfa AF: 0.244 Hom.: 15690

Bravo AF: 0.242

Asia WGS AF: 0.505 AC: 1750 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	13
DANN	Benign	0.63
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs2698530; hg19: chr2-64503895;