rs12998922

Positions:

• chr2-234260381-G-C

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 152,244 control chromosomes in the GnomAD database, including 2,929 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 (2929 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.128

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.251 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26731 AN: 152126 Hom.: 2930 Cov.: 32

Gnomad AFR AF: 0.0628

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.00270

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.176 AC: 26723 AN: 152244 Hom.: 2929 Cov.: 32 AF XY: 0.176 AC XY: 13120 AN XY: 74422

Gnomad4 AFR AF: 0.0627

Gnomad4 AMR AF: 0.257

Gnomad4 ASJ AF: 0.201

Gnomad4 EAS AF: 0.00270

Gnomad4 SAS AF: 0.171

Gnomad4 FIN AF: 0.180

Gnomad4 NFE AF: 0.236

Gnomad4 OTH AF: 0.172

Alfa AF: 0.199 Hom.: 444

Bravo AF: 0.175

Asia WGS AF: 0.0810 AC: 280 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.4
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12998922; hg19: chr2-235169025; COSMIC: COSV69023816;