rs12458349

Positions:

• chr18-62686977-T-G

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;