rs2374671

Variant names:

• chr12-107163334-A-G
• rs2374671

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.548 AC: 22719 AN: 41442

American (AMR) AF: 0.222 AC: 3391 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.121 AC: 418 AN: 3462

East Asian (EAS) AF: 0.287 AC: 1481 AN: 5168

South Asian (SAS) AF: 0.246 AC: 1188 AN: 4826

European-Finnish (FIN) AF: 0.158 AC: 1674 AN: 10590

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.123 AC: 8381 AN: 67976

Other (OTH) AF: 0.219 AC: 462 AN: 2112

Alfa AF: 0.169 Hom.: 14340

Bravo AF: 0.279

Asia WGS AF: 0.283 AC: 984 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	5.5
DANN	Benign	0.59
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs2374671; hg19: chr12-107557112;