rs2374671

Variant names:

• chr12-107163334-A-G
• rs2374671

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 0.262 in 152,046 control chromosomes in the GnomAD database, including 7,841 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 (7841 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.257

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.542 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: 0.262 AC: 39761 AN: 151928 Hom.: 7815 Cov.: 32

Gnomad AFR AF: 0.548

Gnomad AMI AF: 0.0866

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.245

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.220

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

GnomAD4 genome AF: 0.262 AC: 39847 AN: 152046 Hom.: 7841 Cov.: 32 AF XY: 0.264 AC XY: 19622 AN XY: 74322

Gnomad4 AFR AF: 0.548

Gnomad4 AMR AF: 0.222

Gnomad4 ASJ AF: 0.121

Gnomad4 EAS AF: 0.287

Gnomad4 SAS AF: 0.246

Gnomad4 FIN AF: 0.158

Gnomad4 NFE AF: 0.123

Gnomad4 OTH AF: 0.219

Alfa AF: 0.148 Hom.: 4585

Bravo AF: 0.279

Asia WGS AF: 0.283 AC: 984 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	5.5
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2374671; hg19: chr12-107557112;