chr20-17903397-T-C

Variant names:

• chr20-17903397-T-C
• rs8121302

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.342

Gnomad4 AMR AF: 0.364

Gnomad4 ASJ AF: 0.432

Gnomad4 EAS AF: 0.740

Gnomad4 SAS AF: 0.428

Gnomad4 FIN AF: 0.424

Gnomad4 NFE AF: 0.379

Gnomad4 OTH AF: 0.401

Alfa AF: 0.384 Hom.: 5731

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8121302; hg19: chr20-17884041;