chr20-2343645-C-A

Variant names:

• chr20-2343645-C-A
• rs214836

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 0.686 in 151,896 control chromosomes in the GnomAD database, including 37,056 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 0.69 (37056 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.897

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.883 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: 0.686 AC: 104166 AN: 151778 Hom.: 37014 Cov.: 30

Gnomad AFR AF: 0.865

Gnomad AMI AF: 0.437

Gnomad AMR AF: 0.642

Gnomad ASJ AF: 0.485

Gnomad EAS AF: 0.905

Gnomad SAS AF: 0.739

Gnomad FIN AF: 0.640

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.589

Gnomad OTH AF: 0.675

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

GnomAD4 genome AF: 0.686 AC: 104263 AN: 151896 Hom.: 37056 Cov.: 30 AF XY: 0.689 AC XY: 51111 AN XY: 74216

Gnomad4 AFR AF: 0.864

Gnomad4 AMR AF: 0.642

Gnomad4 ASJ AF: 0.485

Gnomad4 EAS AF: 0.904

Gnomad4 SAS AF: 0.739

Gnomad4 FIN AF: 0.640

Gnomad4 NFE AF: 0.589

Gnomad4 OTH AF: 0.676

Alfa AF: 0.654 Hom.: 4161

Bravo AF: 0.696

Asia WGS AF: 0.790 AC: 2744 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.84
DANN	Benign	0.19

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs214836; hg19: chr20-2324291;