20-308352-T-C

Variant names:

• chr20-308352-T-C
• rs6082956

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 0.385 in 152,072 control chromosomes in the GnomAD database, including 11,729 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 0.38 (11729 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.496
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.475 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.385 AC: 58464 AN: 151954 Hom.: 11727 Cov.: 33

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.416

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.428

Gnomad OTH AF: 0.392

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

GnomAD4 genome AF: 0.385 AC: 58480 AN: 152072 Hom.: 11729 Cov.: 33 AF XY: 0.387 AC XY: 28755 AN XY: 74324

African (AFR) AF: 0.280 AC: 11603 AN: 41508

American (AMR) AF: 0.484 AC: 7389 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.366 AC: 1269 AN: 3470

East Asian (EAS) AF: 0.303 AC: 1570 AN: 5184

South Asian (SAS) AF: 0.316 AC: 1521 AN: 4816

European-Finnish (FIN) AF: 0.449 AC: 4741 AN: 10554

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.428 AC: 29089 AN: 67962

Other (OTH) AF: 0.388 AC: 818 AN: 2106

Alfa AF: 0.417 Hom.: 22729

Bravo AF: 0.384

Asia WGS AF: 0.273 AC: 953 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.7
DANN	Benign	0.72
PhyloP100		0.50

Splicing

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

Other links and lift over

dbSNP: rs6082956; hg19: chr20-288996;