rs12998006

Variant names:

• chr2-210804282-T-C
• rs12998006

Your query was ambiguous. Multiple possible variants found:

• chr2-210804282-T-C
• chr2-210804282-T-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 0.236 in 151,912 control chromosomes in the GnomAD database, including 4,691 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 0.24 (4691 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.514

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.276 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: 0.236 AC: 35899 AN: 151794 Hom.: 4689 Cov.: 32

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.359

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.236 AC: 35906 AN: 151912 Hom.: 4691 Cov.: 32 AF XY: 0.239 AC XY: 17769 AN XY: 74242

Gnomad4 AFR AF: 0.130

Gnomad4 AMR AF: 0.278

Gnomad4 ASJ AF: 0.243

Gnomad4 EAS AF: 0.153

Gnomad4 SAS AF: 0.245

Gnomad4 FIN AF: 0.359

Gnomad4 NFE AF: 0.279

Gnomad4 OTH AF: 0.209

Alfa AF: 0.264 Hom.: 1252

Bravo AF: 0.226

Asia WGS AF: 0.185 AC: 646 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.4
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12998006; hg19: chr2-211669006;