6-116784356-T-G

Variant names:

• chr6-116784356-T-G
• rs587771

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.817 AC: 33873 AN: 41438

American (AMR) AF: 0.816 AC: 12459 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.927 AC: 3220 AN: 3472

East Asian (EAS) AF: 0.712 AC: 3674 AN: 5160

South Asian (SAS) AF: 0.884 AC: 4262 AN: 4820

European-Finnish (FIN) AF: 0.770 AC: 8106 AN: 10534

Middle Eastern (MID) AF: 0.901 AC: 265 AN: 294

European-Non Finnish (NFE) AF: 0.798 AC: 54234 AN: 67958

Other (OTH) AF: 0.822 AC: 1740 AN: 2116

Alfa AF: 0.806 Hom.: 106066

Bravo AF: 0.808

Asia WGS AF: 0.804 AC: 2793 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.44
DANN	Benign	0.72
PhyloP100		-0.86

Splicing

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

Other links and lift over

dbSNP: rs587771; hg19: chr6-117105519;