rs2698530

chr2-64276761-A-Cchr2-64276761-A-G

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, non coding transcript 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: ENST00000684810.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.31

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000684810.1	n.339+2714A>C		intron_variant, non_coding_transcript_variant

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;