rs1500038

Positions:

• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;