rs12459138

Variant names:

• chr19-35357437-G-A
• rs12459138

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 0.164 in 152,196 control chromosomes in the GnomAD database, including 2,605 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 0.16 (2605 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.708

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.221 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: 0.165 AC: 25023 AN: 152078 Hom.: 2601 Cov.: 32

Gnomad AFR AF: 0.0554

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.00385

Gnomad SAS AF: 0.222

Gnomad FIN AF: 0.202

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.164 AC: 25035 AN: 152196 Hom.: 2605 Cov.: 32 AF XY: 0.164 AC XY: 12206 AN XY: 74390

Gnomad4 AFR AF: 0.0554

Gnomad4 AMR AF: 0.192

Gnomad4 ASJ AF: 0.212

Gnomad4 EAS AF: 0.00386

Gnomad4 SAS AF: 0.222

Gnomad4 FIN AF: 0.202

Gnomad4 NFE AF: 0.224

Gnomad4 OTH AF: 0.179

Alfa AF: 0.214 Hom.: 5002

Bravo AF: 0.158

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.4
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12459138; hg19: chr19-35848339;