6-129742716-G-A

Variant names:

• chr6-129742716-G-A
• rs208870

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 0.93 in 152,240 control chromosomes in the GnomAD database, including 66,042 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 0.93 (66042 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.995
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.930 AC: 141546 AN: 152122 Hom.: 65991 Cov.: 31

Gnomad AFR AF: 0.880

Gnomad AMI AF: 0.992

Gnomad AMR AF: 0.950

Gnomad ASJ AF: 0.956

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.960

Gnomad FIN AF: 0.937

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.947

Gnomad OTH AF: 0.918

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

GnomAD4 genome AF: 0.930 AC: 141656 AN: 152240 Hom.: 66042 Cov.: 31 AF XY: 0.930 AC XY: 69227 AN XY: 74436

African (AFR) AF: 0.880 AC: 36526 AN: 41514

American (AMR) AF: 0.950 AC: 14528 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.956 AC: 3320 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5189 AN: 5192

South Asian (SAS) AF: 0.960 AC: 4637 AN: 4828

European-Finnish (FIN) AF: 0.937 AC: 9929 AN: 10600

Middle Eastern (MID) AF: 0.837 AC: 246 AN: 294

European-Non Finnish (NFE) AF: 0.947 AC: 64434 AN: 68022

Other (OTH) AF: 0.919 AC: 1944 AN: 2116

Alfa AF: 0.933 Hom.: 50289

Bravo AF: 0.930

Asia WGS AF: 0.972 AC: 3380 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.15
DANN	Benign	0.19
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs208870; hg19: chr6-130063861;