rs6713082

Positions:

• chr2-62289409-C-A
• chr2-62289409-C-G

Variant summary

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

The variant allele was found at a frequency of 0.169 in 152,296 control chromosomes in the GnomAD database, including 2,790 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 0.17 (2790 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.164

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.238 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

Frequencies

GnomAD3 genomes AF: 0.169 AC: 25739 AN: 152178 Hom.: 2798 Cov.: 32

Gnomad AFR AF: 0.0445

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.279

Gnomad EAS AF: 0.0102

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.169 AC: 25715 AN: 152296 Hom.: 2790 Cov.: 32 AF XY: 0.166 AC XY: 12362 AN XY: 74456

Gnomad4 AFR AF: 0.0444

Gnomad4 AMR AF: 0.199

Gnomad4 ASJ AF: 0.279

Gnomad4 EAS AF: 0.0102

Gnomad4 SAS AF: 0.138

Gnomad4 FIN AF: 0.204

Gnomad4 NFE AF: 0.241

Gnomad4 OTH AF: 0.180

Alfa AF: 0.228 Hom.: 5611

Bravo AF: 0.164

Asia WGS AF: 0.0710 AC: 248 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.1
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6713082; hg19: chr2-62516544;