rs1893146

Positions:

• chr18-8987429-G-A
• chr18-8987429-G-T

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 0.122 in 152,158 control chromosomes in the GnomAD database, including 1,267 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 0.12 (1267 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.42

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.289 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: 0.122 AC: 18563 AN: 152040 Hom.: 1265 Cov.: 33

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.0614

Gnomad AMR AF: 0.0986

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.122 AC: 18582 AN: 152158 Hom.: 1267 Cov.: 33 AF XY: 0.124 AC XY: 9210 AN XY: 74388

Gnomad4 AFR AF: 0.112

Gnomad4 AMR AF: 0.0984

Gnomad4 ASJ AF: 0.101

Gnomad4 EAS AF: 0.301

Gnomad4 SAS AF: 0.151

Gnomad4 FIN AF: 0.104

Gnomad4 NFE AF: 0.123

Gnomad4 OTH AF: 0.138

Alfa AF: 0.111 Hom.: 1029

Bravo AF: 0.119

Asia WGS AF: 0.217 AC: 752 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.012
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1893146; hg19: chr18-8987427;