20-5696137-C-T

Variant names:

• chr20-5696137-C-T
• rs805764

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 0.197 in 152,152 control chromosomes in the GnomAD database, including 3,858 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 0.20 (3858 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.597
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.26 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: 0.197 AC: 30019 AN: 152034 Hom.: 3855 Cov.: 32

Gnomad AFR AF: 0.0467

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.199

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.388

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.264

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.197 AC: 30024 AN: 152152 Hom.: 3858 Cov.: 32 AF XY: 0.202 AC XY: 14989 AN XY: 74344

African (AFR) AF: 0.0466 AC: 1937 AN: 41572

American (AMR) AF: 0.183 AC: 2787 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.155 AC: 537 AN: 3468

East Asian (EAS) AF: 0.199 AC: 1032 AN: 5190

South Asian (SAS) AF: 0.220 AC: 1062 AN: 4822

European-Finnish (FIN) AF: 0.388 AC: 4091 AN: 10550

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.264 AC: 17918 AN: 67982

Other (OTH) AF: 0.192 AC: 405 AN: 2110

Alfa AF: 0.237 Hom.: 4343

Bravo AF: 0.177

Asia WGS AF: 0.202 AC: 703 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.33
DANN	Benign	0.74
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs805764; hg19: chr20-5676783; COSMIC: COSV66932324;