20-5114675-C-G

Variant names:

• chr20-5114675-C-G
• rs3729558

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 0.592 in 152,050 control chromosomes in the GnomAD database, including 28,370 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 0.59 (28370 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.275
• Publications: 9 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 (AFR) allele frequency at 95% confidence interval = 0.795 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: 0.592 AC: 89876 AN: 151932 Hom.: 28327 Cov.: 33

Gnomad AFR AF: 0.802

Gnomad AMI AF: 0.545

Gnomad AMR AF: 0.458

Gnomad ASJ AF: 0.681

Gnomad EAS AF: 0.327

Gnomad SAS AF: 0.713

Gnomad FIN AF: 0.394

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.532

Gnomad OTH AF: 0.583

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

GnomAD4 genome AF: 0.592 AC: 89979 AN: 152050 Hom.: 28370 Cov.: 33 AF XY: 0.585 AC XY: 43454 AN XY: 74316

African (AFR) AF: 0.802 AC: 33276 AN: 41500

American (AMR) AF: 0.457 AC: 6980 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.681 AC: 2364 AN: 3472

East Asian (EAS) AF: 0.328 AC: 1694 AN: 5170

South Asian (SAS) AF: 0.711 AC: 3432 AN: 4824

European-Finnish (FIN) AF: 0.394 AC: 4152 AN: 10534

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.532 AC: 36134 AN: 67978

Other (OTH) AF: 0.589 AC: 1242 AN: 2110

Alfa AF: 0.374 Hom.: 839

Bravo AF: 0.597

Asia WGS AF: 0.573 AC: 1995 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.28
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs3729558; hg19: chr20-5095321;