rs802718

chr6-127968366-G-Achr6-127968366-G-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 0.872 in 152,200 control chromosomes in the GnomAD database, including 58,494 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 0.87 (58494 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.235

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.906 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: 0.872 AC: 132589 AN: 152082 Hom.: 58459 Cov.: 32

Gnomad AFR AF: 0.905

Gnomad AMI AF: 0.837

Gnomad AMR AF: 0.816

Gnomad ASJ AF: 0.922

Gnomad EAS AF: 0.461

Gnomad SAS AF: 0.679

Gnomad FIN AF: 0.836

Gnomad MID AF: 0.911

Gnomad NFE AF: 0.913

Gnomad OTH AF: 0.869

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

GnomAD4 genome AF: 0.872 AC: 132674 AN: 152200 Hom.: 58494 Cov.: 32 AF XY: 0.861 AC XY: 64063 AN XY: 74394

Gnomad4 AFR AF: 0.904

Gnomad4 AMR AF: 0.816

Gnomad4 ASJ AF: 0.922

Gnomad4 EAS AF: 0.462

Gnomad4 SAS AF: 0.680

Gnomad4 FIN AF: 0.836

Gnomad4 NFE AF: 0.913

Gnomad4 OTH AF: 0.861

Alfa AF: 0.899 Hom.: 105696

Bravo AF: 0.873

Asia WGS AF: 0.577 AC: 2004 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	1.7
Dann	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs802718; hg19: chr6-128289511;