rs12458349

Variant names:

• chr18-62686977-T-G
• rs12458349

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 0.0408 in 152,338 control chromosomes in the GnomAD database, including 189 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 0.041 (189 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00700

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.49).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.063 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: 0.0408 AC: 6210 AN: 152220 Hom.: 189 Cov.: 31

Gnomad AFR AF: 0.0111

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.0329

Gnomad ASJ AF: 0.0354

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0257

Gnomad FIN AF: 0.0433

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0646

Gnomad OTH AF: 0.0406

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

GnomAD4 genome AF: 0.0408 AC: 6211 AN: 152338 Hom.: 189 Cov.: 31 AF XY: 0.0386 AC XY: 2876 AN XY: 74498

Gnomad4 AFR AF: 0.0110

Gnomad4 AMR AF: 0.0329

Gnomad4 ASJ AF: 0.0354

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.0257

Gnomad4 FIN AF: 0.0433

Gnomad4 NFE AF: 0.0646

Gnomad4 OTH AF: 0.0416

Alfa AF: 0.0562 Hom.: 130

Bravo AF: 0.0383

Asia WGS AF: 0.0320 AC: 112 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	13
DANN	Benign	0.92

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12458349; hg19: chr18-60354210;