rs12518307

Variant names:

• chr5-24684017-A-G
• rs12518307

Your query was ambiguous. Multiple possible variants found:

• chr5-24684017-A-G
• chr5-24684017-A-T

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 0.689 in 152,038 control chromosomes in the GnomAD database, including 36,572 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 0.69 (36572 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.739 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: 0.689 AC: 104699 AN: 151920 Hom.: 36545 Cov.: 32

Gnomad AFR AF: 0.600

Gnomad AMI AF: 0.928

Gnomad AMR AF: 0.661

Gnomad ASJ AF: 0.815

Gnomad EAS AF: 0.523

Gnomad SAS AF: 0.725

Gnomad FIN AF: 0.717

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.744

Gnomad OTH AF: 0.719

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

GnomAD4 genome AF: 0.689 AC: 104768 AN: 152038 Hom.: 36572 Cov.: 32 AF XY: 0.688 AC XY: 51132 AN XY: 74308

African (AFR) AF: 0.601 AC: 24905 AN: 41470

American (AMR) AF: 0.661 AC: 10092 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.815 AC: 2829 AN: 3472

East Asian (EAS) AF: 0.523 AC: 2689 AN: 5138

South Asian (SAS) AF: 0.726 AC: 3497 AN: 4820

European-Finnish (FIN) AF: 0.717 AC: 7567 AN: 10560

Middle Eastern (MID) AF: 0.833 AC: 245 AN: 294

European-Non Finnish (NFE) AF: 0.744 AC: 50584 AN: 67988

Other (OTH) AF: 0.718 AC: 1514 AN: 2108

Alfa AF: 0.695 Hom.: 4381

Bravo AF: 0.684

Asia WGS AF: 0.605 AC: 2108 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.33
DANN	Benign	0.67
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs12518307; hg19: chr5-24684126;