rs12187724

Variant names:

• chr5-25934961-A-C
• rs12187724

Your query was ambiguous. Multiple possible variants found:

• chr5-25934961-A-C
• chr5-25934961-A-G
• chr5-25934961-A-T

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 0.341 in 151,954 control chromosomes in the GnomAD database, including 9,239 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 0.34 (9239 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.19

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.563 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: 0.342 AC: 51854 AN: 151834 Hom.: 9242 Cov.: 32

Gnomad AFR AF: 0.253

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.374

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.580

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.341 AC: 51878 AN: 151954 Hom.: 9239 Cov.: 32 AF XY: 0.345 AC XY: 25636 AN XY: 74254

Gnomad4 AFR AF: 0.253

Gnomad4 AMR AF: 0.374

Gnomad4 ASJ AF: 0.343

Gnomad4 EAS AF: 0.580

Gnomad4 SAS AF: 0.464

Gnomad4 FIN AF: 0.332

Gnomad4 NFE AF: 0.363

Gnomad4 OTH AF: 0.350

Alfa AF: 0.355 Hom.: 16272

Bravo AF: 0.338

Asia WGS AF: 0.485 AC: 1670 AN: 3450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	9.5
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12187724; hg19: chr5-25935070;