rs12990515

Variant names:

• chr2-41173919-T-C
• rs12990515

Your query was ambiguous. Multiple possible variants found:

• chr2-41173919-T-C
• chr2-41173919-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 0.238 in 152,052 control chromosomes in the GnomAD database, including 4,527 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 (4527 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0510

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.269 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: 0.239 AC: 36238 AN: 151932 Hom.: 4530 Cov.: 32

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.297

Gnomad EAS AF: 0.0386

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.281

Gnomad MID AF: 0.239

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.238 AC: 36249 AN: 152052 Hom.: 4527 Cov.: 32 AF XY: 0.236 AC XY: 17555 AN XY: 74310

Gnomad4 AFR AF: 0.215

Gnomad4 AMR AF: 0.186

Gnomad4 ASJ AF: 0.297

Gnomad4 EAS AF: 0.0387

Gnomad4 SAS AF: 0.209

Gnomad4 FIN AF: 0.281

Gnomad4 NFE AF: 0.272

Gnomad4 OTH AF: 0.213

Alfa AF: 0.154 Hom.: 394

Bravo AF: 0.227

Asia WGS AF: 0.120 AC: 415 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	9.5
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12990515; hg19: chr2-41401059;