rs20349

Variant names:

• chr2-133818678-G-T
• rs20349

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 0.342 in 152,052 control chromosomes in the GnomAD database, including 9,262 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 0.34 (9262 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.271

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.387 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: 0.342 AC: 52000 AN: 151932 Hom.: 9262 Cov.: 33

Gnomad AFR AF: 0.393

Gnomad AMI AF: 0.427

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.501

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.258

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.394

Gnomad NFE AF: 0.337

Gnomad OTH AF: 0.352

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

GnomAD4 genome AF: 0.342 AC: 52021 AN: 152052 Hom.: 9262 Cov.: 33 AF XY: 0.339 AC XY: 25223 AN XY: 74336

Gnomad4 AFR AF: 0.392

Gnomad4 AMR AF: 0.271

Gnomad4 ASJ AF: 0.501

Gnomad4 EAS AF: 0.159

Gnomad4 SAS AF: 0.257

Gnomad4 FIN AF: 0.344

Gnomad4 NFE AF: 0.337

Gnomad4 OTH AF: 0.350

Alfa AF: 0.341 Hom.: 18486

Bravo AF: 0.340

Asia WGS AF: 0.188 AC: 656 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.1
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs20349; hg19: chr2-134576249;