rs2118137

Variant names:

• chr12-66263872-C-G
• rs2118137

Your query was ambiguous. Multiple possible variants found:

• chr12-66263872-C-G
• chr12-66263872-C-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 0.435 in 152,042 control chromosomes in the GnomAD database, including 15,243 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 0.44 (15243 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.234

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.516 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: 0.435 AC: 66134 AN: 151922 Hom.: 15248 Cov.: 32

Gnomad AFR AF: 0.338

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.155

Gnomad SAS AF: 0.431

Gnomad FIN AF: 0.399

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.521

Gnomad OTH AF: 0.467

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

GnomAD4 genome AF: 0.435 AC: 66156 AN: 152042 Hom.: 15243 Cov.: 32 AF XY: 0.429 AC XY: 31866 AN XY: 74300

Gnomad4 AFR AF: 0.338

Gnomad4 AMR AF: 0.404

Gnomad4 ASJ AF: 0.518

Gnomad4 EAS AF: 0.154

Gnomad4 SAS AF: 0.431

Gnomad4 FIN AF: 0.399

Gnomad4 NFE AF: 0.521

Gnomad4 OTH AF: 0.462

Alfa AF: 0.323 Hom.: 830

Bravo AF: 0.431

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	2.8
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2118137; hg19: chr12-66657652; COSMIC: COSV66915184;