20-187379-T-C

Variant names:

• chr20-187379-T-C
• rs13036722

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 0.158 in 151,990 control chromosomes in the GnomAD database, including 2,404 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 0.16 (2404 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.635

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.281 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: 0.158 AC: 23999 AN: 151872 Hom.: 2395 Cov.: 32

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.00560

Gnomad SAS AF: 0.0847

Gnomad FIN AF: 0.0660

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.158 AC: 24043 AN: 151990 Hom.: 2404 Cov.: 32 AF XY: 0.154 AC XY: 11439 AN XY: 74304

Gnomad4 AFR AF: 0.285

Gnomad4 AMR AF: 0.109

Gnomad4 ASJ AF: 0.126

Gnomad4 EAS AF: 0.00561

Gnomad4 SAS AF: 0.0844

Gnomad4 FIN AF: 0.0660

Gnomad4 NFE AF: 0.125

Gnomad4 OTH AF: 0.137

Alfa AF: 0.136 Hom.: 485

Bravo AF: 0.165

Asia WGS AF: 0.0790 AC: 276 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.2
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13036722; hg19: chr20-168020;