chr2-64276761-A-C

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000684810.1(ENSG00000288932):​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: ENSG00000288932 ENST00000684810.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.31

Genes affected

ENSG00000288932 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288932	ENST00000684810.1	n.339+2714A>C		intron_variant	Intron 1 of 1
ENSG00000288932	ENST00000686684.1	n.266+2714A>C		intron_variant	Intron 1 of 1
ENSG00000288932	ENST00000689610.1	n.245+2714A>C		intron_variant	Intron 1 of 1

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

Gnomad4 AFR AF: 0.150

Gnomad4 AMR AF: 0.304

Gnomad4 ASJ AF: 0.262

Gnomad4 EAS AF: 0.627

Gnomad4 SAS AF: 0.414

Gnomad4 FIN AF: 0.217

Gnomad4 NFE AF: 0.237

Gnomad4 OTH AF: 0.258

Alfa AF: 0.242 Hom.: 6169

Bravo AF: 0.242

Asia WGS AF: 0.505 AC: 1750 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2698530; hg19: chr2-64503895;