chr20-6934267-T-C

Variant names:

• chr20-6934267-T-C
• rs717087

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 0.792 in 152,124 control chromosomes in the GnomAD database, including 48,327 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 0.79 (48327 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.298
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.841 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: 0.792 AC: 120352 AN: 152006 Hom.: 48299 Cov.: 33

Gnomad AFR AF: 0.700

Gnomad AMI AF: 0.937

Gnomad AMR AF: 0.844

Gnomad ASJ AF: 0.788

Gnomad EAS AF: 0.499

Gnomad SAS AF: 0.702

Gnomad FIN AF: 0.899

Gnomad MID AF: 0.783

Gnomad NFE AF: 0.846

Gnomad OTH AF: 0.783

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

GnomAD4 genome AF: 0.792 AC: 120435 AN: 152124 Hom.: 48327 Cov.: 33 AF XY: 0.791 AC XY: 58816 AN XY: 74386

African (AFR) AF: 0.700 AC: 29047 AN: 41518

American (AMR) AF: 0.845 AC: 12927 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.788 AC: 2729 AN: 3464

East Asian (EAS) AF: 0.499 AC: 2576 AN: 5166

South Asian (SAS) AF: 0.704 AC: 3387 AN: 4814

European-Finnish (FIN) AF: 0.899 AC: 9499 AN: 10568

Middle Eastern (MID) AF: 0.784 AC: 229 AN: 292

European-Non Finnish (NFE) AF: 0.847 AC: 57540 AN: 67974

Other (OTH) AF: 0.780 AC: 1648 AN: 2112

Alfa AF: 0.810 Hom.: 6674

Bravo AF: 0.786

Asia WGS AF: 0.635 AC: 2194 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.1
DANN	Benign	0.81
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs717087; hg19: chr20-6914914;