20-17903397-T-C

Variant names:

• chr20-17903397-T-C
• rs8121302

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 0.387 in 151,796 control chromosomes in the GnomAD database, including 11,841 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 0.39 (11841 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.151
• Publications: 4 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 (EAS) allele frequency at 95% confidence interval = 0.72 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: 0.387 AC: 58648 AN: 151678 Hom.: 11836 Cov.: 31

Gnomad AFR AF: 0.342

Gnomad AMI AF: 0.451

Gnomad AMR AF: 0.364

Gnomad ASJ AF: 0.432

Gnomad EAS AF: 0.740

Gnomad SAS AF: 0.428

Gnomad FIN AF: 0.424

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.379

Gnomad OTH AF: 0.397

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

GnomAD4 genome AF: 0.387 AC: 58693 AN: 151796 Hom.: 11841 Cov.: 31 AF XY: 0.391 AC XY: 28987 AN XY: 74144

African (AFR) AF: 0.342 AC: 14155 AN: 41382

American (AMR) AF: 0.364 AC: 5539 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.432 AC: 1496 AN: 3466

East Asian (EAS) AF: 0.740 AC: 3811 AN: 5152

South Asian (SAS) AF: 0.428 AC: 2057 AN: 4810

European-Finnish (FIN) AF: 0.424 AC: 4458 AN: 10518

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.379 AC: 25778 AN: 67934

Other (OTH) AF: 0.401 AC: 843 AN: 2102

Alfa AF: 0.382 Hom.: 6339

Bravo AF: 0.380

Asia WGS AF: 0.568 AC: 1978 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.7
DANN	Benign	0.68
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs8121302; hg19: chr20-17884041;