20-40868199-G-A

Variant names:

• chr20-40868199-G-A
• rs875627

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 0.621 in 152,182 control chromosomes in the GnomAD database, including 30,800 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 0.62 (30800 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.815 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: 0.621 AC: 94393 AN: 152066 Hom.: 30744 Cov.: 33

Gnomad AFR AF: 0.821

Gnomad AMI AF: 0.485

Gnomad AMR AF: 0.459

Gnomad ASJ AF: 0.561

Gnomad EAS AF: 0.461

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.590

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.573

Gnomad OTH AF: 0.590

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

GnomAD4 genome AF: 0.621 AC: 94510 AN: 152182 Hom.: 30800 Cov.: 33 AF XY: 0.611 AC XY: 45459 AN XY: 74404

African (AFR) AF: 0.822 AC: 34146 AN: 41544

American (AMR) AF: 0.458 AC: 7014 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.561 AC: 1948 AN: 3472

East Asian (EAS) AF: 0.461 AC: 2383 AN: 5174

South Asian (SAS) AF: 0.408 AC: 1968 AN: 4826

European-Finnish (FIN) AF: 0.590 AC: 6241 AN: 10576

Middle Eastern (MID) AF: 0.524 AC: 153 AN: 292

European-Non Finnish (NFE) AF: 0.573 AC: 38965 AN: 67972

Other (OTH) AF: 0.592 AC: 1250 AN: 2110

Alfa AF: 0.586 Hom.: 65088

Bravo AF: 0.623

Asia WGS AF: 0.450 AC: 1566 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.43
DANN	Benign	0.42
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs875627; hg19: chr20-39496839;