6-2936688-G-T

Variant names:

• chr6-2936688-G-T
• rs318452

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 0.511 in 151,592 control chromosomes in the GnomAD database, including 20,309 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 0.51 (20309 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.713 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: 0.511 AC: 77401 AN: 151472 Hom.: 20264 Cov.: 33

Gnomad AFR AF: 0.581

Gnomad AMI AF: 0.384

Gnomad AMR AF: 0.567

Gnomad ASJ AF: 0.521

Gnomad EAS AF: 0.733

Gnomad SAS AF: 0.518

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.545

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

GnomAD4 genome AF: 0.511 AC: 77498 AN: 151592 Hom.: 20309 Cov.: 33 AF XY: 0.510 AC XY: 37774 AN XY: 74064

Gnomad4 AFR AF: 0.581

Gnomad4 AMR AF: 0.568

Gnomad4 ASJ AF: 0.521

Gnomad4 EAS AF: 0.732

Gnomad4 SAS AF: 0.517

Gnomad4 FIN AF: 0.396

Gnomad4 NFE AF: 0.456

Gnomad4 OTH AF: 0.544

Alfa AF: 0.349 Hom.: 920

Bravo AF: 0.529

Asia WGS AF: 0.636 AC: 2210 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.36
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs318452; hg19: chr6-2936922;