rs6937815

chr6-132424824-G-Achr6-132424824-G-T

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 0.0649 in 152,070 control chromosomes in the GnomAD database, including 692 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 0.065 (692 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.545

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.378 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: 0.0649 AC: 9868 AN: 151952 Hom.: 695 Cov.: 32

Gnomad AFR AF: 0.0400

Gnomad AMI AF: 0.0187

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.0646

Gnomad EAS AF: 0.392

Gnomad SAS AF: 0.0328

Gnomad FIN AF: 0.0287

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0477

Gnomad OTH AF: 0.0695

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

GnomAD4 genome AF: 0.0649 AC: 9872 AN: 152070 Hom.: 692 Cov.: 32 AF XY: 0.0677 AC XY: 5029 AN XY: 74336

Gnomad4 AFR AF: 0.0400

Gnomad4 AMR AF: 0.136

Gnomad4 ASJ AF: 0.0646

Gnomad4 EAS AF: 0.393

Gnomad4 SAS AF: 0.0326

Gnomad4 FIN AF: 0.0287

Gnomad4 NFE AF: 0.0477

Gnomad4 OTH AF: 0.0693

Alfa AF: 0.0203 Hom.: 23

Bravo AF: 0.0750

Asia WGS AF: 0.169 AC: 587 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	2.0
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6937815; hg19: chr6-132745963;