rs12515012

Variant names:

• chr5-44694433-G-A
• rs12515012

Your query was ambiguous. Multiple possible variants found:

• chr5-44694433-G-A
• chr5-44694433-G-C
• chr5-44694433-G-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 0.401 in 152,022 control chromosomes in the GnomAD database, including 12,479 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 0.40 (12479 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365

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 (EAS) allele frequency at 95% confidence interval = 0.488 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: 0.401 AC: 60890 AN: 151904 Hom.: 12454 Cov.: 32

Gnomad AFR AF: 0.363

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.448

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.504

Gnomad SAS AF: 0.499

Gnomad FIN AF: 0.395

Gnomad MID AF: 0.439

Gnomad NFE AF: 0.399

Gnomad OTH AF: 0.408

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

GnomAD4 genome AF: 0.401 AC: 60937 AN: 152022 Hom.: 12479 Cov.: 32 AF XY: 0.406 AC XY: 30169 AN XY: 74306

Gnomad4 AFR AF: 0.363

Gnomad4 AMR AF: 0.449

Gnomad4 ASJ AF: 0.427

Gnomad4 EAS AF: 0.504

Gnomad4 SAS AF: 0.499

Gnomad4 FIN AF: 0.395

Gnomad4 NFE AF: 0.399

Gnomad4 OTH AF: 0.414

Alfa AF: 0.406 Hom.: 1572

Bravo AF: 0.402

Asia WGS AF: 0.510 AC: 1773 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	1.3
DANN	Benign	0.17

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12515012; hg19: chr5-44694535;