rs2647050

chr6-32701990-T-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;