rs1500038

Variant names:

• chr12-59148374-G-A
• rs1500038

Your query was ambiguous. Multiple possible variants found:

• chr12-59148374-G-A
• chr12-59148374-G-C

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 0.832 in 151,636 control chromosomes in the GnomAD database, including 52,604 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 0.83 (52604 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.118

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.874 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: 0.832 AC: 126064 AN: 151520 Hom.: 52565 Cov.: 28

Gnomad AFR AF: 0.882

Gnomad AMI AF: 0.889

Gnomad AMR AF: 0.823

Gnomad ASJ AF: 0.884

Gnomad EAS AF: 0.856

Gnomad SAS AF: 0.753

Gnomad FIN AF: 0.816

Gnomad MID AF: 0.883

Gnomad NFE AF: 0.806

Gnomad OTH AF: 0.849

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

GnomAD4 genome AF: 0.832 AC: 126159 AN: 151636 Hom.: 52604 Cov.: 28 AF XY: 0.832 AC XY: 61614 AN XY: 74016

Gnomad4 AFR AF: 0.882

Gnomad4 AMR AF: 0.823

Gnomad4 ASJ AF: 0.884

Gnomad4 EAS AF: 0.857

Gnomad4 SAS AF: 0.752

Gnomad4 FIN AF: 0.816

Gnomad4 NFE AF: 0.806

Gnomad4 OTH AF: 0.844

Alfa AF: 0.761 Hom.: 2258

Bravo AF: 0.839

Asia WGS AF: 0.814 AC: 2831 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.59
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1500038; hg19: chr12-59542155;