rs2647050

Variant names:

• chr6-32701990-T-C
• rs2647050

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 0.365 in 145,436 control chromosomes in the GnomAD database, including 9,732 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 0.37 (9732 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.51

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.521 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

Frequencies

GnomAD3 genomes AF: 0.366 AC: 53131 AN: 145322 Hom.: 9734 Cov.: 32

Gnomad AFR AF: 0.356

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.466

Gnomad EAS AF: 0.539

Gnomad SAS AF: 0.484

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.539

Gnomad NFE AF: 0.362

Gnomad OTH AF: 0.413

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

GnomAD4 genome AF: 0.365 AC: 53143 AN: 145436 Hom.: 9732 Cov.: 32 AF XY: 0.362 AC XY: 25575 AN XY: 70692

Gnomad4 AFR AF: 0.356

Gnomad4 AMR AF: 0.374

Gnomad4 ASJ AF: 0.466

Gnomad4 EAS AF: 0.538

Gnomad4 SAS AF: 0.481

Gnomad4 FIN AF: 0.215

Gnomad4 NFE AF: 0.362

Gnomad4 OTH AF: 0.417

Alfa AF: 0.373 Hom.: 15643

Bravo AF: 0.360

Asia WGS AF: 0.492 AC: 1709 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.1
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2647050; hg19: chr6-32669767;