6-116784356-T-G

Variant names:

• chr6-116784356-T-G
• rs587771

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 0.807 in 151,980 control chromosomes in the GnomAD database, including 49,578 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 0.81 (49578 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.861

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.862 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: 0.807 AC: 122548 AN: 151862 Hom.: 49543 Cov.: 31

Gnomad AFR AF: 0.817

Gnomad AMI AF: 0.879

Gnomad AMR AF: 0.816

Gnomad ASJ AF: 0.927

Gnomad EAS AF: 0.712

Gnomad SAS AF: 0.885

Gnomad FIN AF: 0.770

Gnomad MID AF: 0.899

Gnomad NFE AF: 0.798

Gnomad OTH AF: 0.824

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

GnomAD4 genome AF: 0.807 AC: 122635 AN: 151980 Hom.: 49578 Cov.: 31 AF XY: 0.805 AC XY: 59806 AN XY: 74284

Gnomad4 AFR AF: 0.817

Gnomad4 AMR AF: 0.816

Gnomad4 ASJ AF: 0.927

Gnomad4 EAS AF: 0.712

Gnomad4 SAS AF: 0.884

Gnomad4 FIN AF: 0.770

Gnomad4 NFE AF: 0.798

Gnomad4 OTH AF: 0.822

Alfa AF: 0.807 Hom.: 67792

Bravo AF: 0.808

Asia WGS AF: 0.804 AC: 2793 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.44
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs587771; hg19: chr6-117105519;