rs1342842

Variant names:

• chr20-232882-A-C
• rs1342842

Your query was ambiguous. Multiple possible variants found:

• chr20-232882-A-C
• chr20-232882-A-G
• chr20-232882-A-T

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 0.176 in 152,122 control chromosomes in the GnomAD database, including 3,426 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 0.18 (3426 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.355 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: 0.176 AC: 26757 AN: 152004 Hom.: 3422 Cov.: 32

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.0340

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.0424

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0911

Gnomad OTH AF: 0.148

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

GnomAD4 genome AF: 0.176 AC: 26780 AN: 152122 Hom.: 3426 Cov.: 32 AF XY: 0.176 AC XY: 13098 AN XY: 74364

Gnomad4 AFR AF: 0.359

Gnomad4 AMR AF: 0.125

Gnomad4 ASJ AF: 0.0424

Gnomad4 EAS AF: 0.187

Gnomad4 SAS AF: 0.183

Gnomad4 FIN AF: 0.133

Gnomad4 NFE AF: 0.0911

Gnomad4 OTH AF: 0.146

Alfa AF: 0.0867 Hom.: 349

Bravo AF: 0.181

Asia WGS AF: 0.195 AC: 676 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	0.20
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: rs1342842; hg19: chr20-213523;