20-39943772-C-T

Variant names:

• chr20-39943772-C-T
• rs55734731

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 0.0977 in 152,160 control chromosomes in the GnomAD database, including 931 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 0.098 (931 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0110
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.195 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: 0.0979 AC: 14879 AN: 152042 Hom.: 930 Cov.: 32

Gnomad AFR AF: 0.0264

Gnomad AMI AF: 0.0768

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.0942

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.0795

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.0977 AC: 14867 AN: 152160 Hom.: 931 Cov.: 32 AF XY: 0.0969 AC XY: 7207 AN XY: 74382

African (AFR) AF: 0.0263 AC: 1091 AN: 41516

American (AMR) AF: 0.164 AC: 2501 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0942 AC: 327 AN: 3470

East Asian (EAS) AF: 0.206 AC: 1064 AN: 5172

South Asian (SAS) AF: 0.0792 AC: 382 AN: 4826

European-Finnish (FIN) AF: 0.105 AC: 1110 AN: 10584

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.119 AC: 8075 AN: 68000

Other (OTH) AF: 0.110 AC: 233 AN: 2114

Alfa AF: 0.0488 Hom.: 42

Bravo AF: 0.104

Asia WGS AF: 0.107 AC: 374 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.0
DANN	Benign	0.62
PhyloP100		0.011

Splicing

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

Other links and lift over

dbSNP: rs55734731; hg19: chr20-38572414;