rs507779

Positions:

• chr6-137642455-C-A

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 0.265 in 151,894 control chromosomes in the GnomAD database, including 5,641 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 0.26 (5641 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.137

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.346 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.265 AC: 40183 AN: 151774 Hom.: 5623 Cov.: 31

Gnomad AFR AF: 0.351

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.360

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.245

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

GnomAD4 genome AF: 0.265 AC: 40241 AN: 151894 Hom.: 5641 Cov.: 31 AF XY: 0.261 AC XY: 19410 AN XY: 74236

Gnomad4 AFR AF: 0.351

Gnomad4 AMR AF: 0.201

Gnomad4 ASJ AF: 0.245

Gnomad4 EAS AF: 0.359

Gnomad4 SAS AF: 0.249

Gnomad4 FIN AF: 0.204

Gnomad4 NFE AF: 0.232

Gnomad4 OTH AF: 0.242

Alfa AF: 0.235 Hom.: 812

Bravo AF: 0.266

Asia WGS AF: 0.278 AC: 964 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.1
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs507779; hg19: chr6-137963592;