rs2002842

Variant names:

• chr18-78649597-C-A
• rs2002842

Your query was ambiguous. Multiple possible variants found:

• chr18-78649597-C-A
• chr18-78649597-C-G

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 0.412 in 152,100 control chromosomes in the GnomAD database, including 13,767 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 0.41 (13767 hom., cov: 34)
• 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.802 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: 0.412 AC: 62583 AN: 151982 Hom.: 13757 Cov.: 34

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.244

Gnomad AMR AF: 0.501

Gnomad ASJ AF: 0.360

Gnomad EAS AF: 0.823

Gnomad SAS AF: 0.470

Gnomad FIN AF: 0.419

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.418

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.412 AC: 62624 AN: 152100 Hom.: 13767 Cov.: 34 AF XY: 0.421 AC XY: 31279 AN XY: 74384

Gnomad4 AFR AF: 0.316

Gnomad4 AMR AF: 0.501

Gnomad4 ASJ AF: 0.360

Gnomad4 EAS AF: 0.823

Gnomad4 SAS AF: 0.468

Gnomad4 FIN AF: 0.419

Gnomad4 NFE AF: 0.418

Gnomad4 OTH AF: 0.440

Alfa AF: 0.426 Hom.: 22833

Bravo AF: 0.414

Asia WGS AF: 0.647 AC: 2244 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.6
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: rs2002842; hg19: chr18-76409597; COSMIC: COSV58350784;