20-6990184-C-T

Variant names:

• chr20-6990184-C-T
• rs952793

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 0.224 in 151,894 control chromosomes in the GnomAD database, including 5,033 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 0.22 (5033 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0160
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.423 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.224 AC: 33979 AN: 151776 Hom.: 5027 Cov.: 31

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.219

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.0675

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.224 AC: 34020 AN: 151894 Hom.: 5033 Cov.: 31 AF XY: 0.219 AC XY: 16244 AN XY: 74260

African (AFR) AF: 0.428 AC: 17711 AN: 41370

American (AMR) AF: 0.144 AC: 2196 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.156 AC: 541 AN: 3464

East Asian (EAS) AF: 0.0674 AC: 347 AN: 5146

South Asian (SAS) AF: 0.188 AC: 906 AN: 4816

European-Finnish (FIN) AF: 0.113 AC: 1196 AN: 10546

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.154 AC: 10468 AN: 67966

Other (OTH) AF: 0.196 AC: 414 AN: 2108

Alfa AF: 0.156 Hom.: 1166

Bravo AF: 0.235

Asia WGS AF: 0.168 AC: 585 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.7
DANN	Benign	0.57
PhyloP100		-0.016

Splicing

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

Other links and lift over

dbSNP: rs952793; hg19: chr20-6970831;