rs2374951

Variant names:

• chr12-108058887-A-G
• rs2374951

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 0.258 in 152,164 control chromosomes in the GnomAD database, including 5,587 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 0.26 (5587 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.138

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.368 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: 0.257 AC: 39133 AN: 152044 Hom.: 5562 Cov.: 33

Gnomad AFR AF: 0.373

Gnomad AMI AF: 0.304

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.159

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.220

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.222

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.258 AC: 39194 AN: 152164 Hom.: 5587 Cov.: 33 AF XY: 0.257 AC XY: 19118 AN XY: 74376

Gnomad4 AFR AF: 0.373

Gnomad4 AMR AF: 0.218

Gnomad4 ASJ AF: 0.151

Gnomad4 EAS AF: 0.159

Gnomad4 SAS AF: 0.158

Gnomad4 FIN AF: 0.220

Gnomad4 NFE AF: 0.222

Gnomad4 OTH AF: 0.237

Alfa AF: 0.235 Hom.: 1010

Bravo AF: 0.262

Asia WGS AF: 0.163 AC: 568 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.3
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2374951; hg19: chr12-108452664;