rs1398193

Variant names:

• chr18-48460768-T-A
• rs1398193

Your query was ambiguous. Multiple possible variants found:

• chr18-48460768-T-A
• chr18-48460768-T-C
• chr18-48460768-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 0.826 in 152,112 control chromosomes in the GnomAD database, including 53,355 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 (53355 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.528

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.933 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: 0.826 AC: 125580 AN: 151994 Hom.: 53330 Cov.: 31

Gnomad AFR AF: 0.618

Gnomad AMI AF: 0.959

Gnomad AMR AF: 0.809

Gnomad ASJ AF: 0.869

Gnomad EAS AF: 0.808

Gnomad SAS AF: 0.853

Gnomad FIN AF: 0.908

Gnomad MID AF: 0.892

Gnomad NFE AF: 0.939

Gnomad OTH AF: 0.848

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

GnomAD4 genome AF: 0.826 AC: 125650 AN: 152112 Hom.: 53355 Cov.: 31 AF XY: 0.824 AC XY: 61232 AN XY: 74344

Gnomad4 AFR AF: 0.617

Gnomad4 AMR AF: 0.809

Gnomad4 ASJ AF: 0.869

Gnomad4 EAS AF: 0.808

Gnomad4 SAS AF: 0.853

Gnomad4 FIN AF: 0.908

Gnomad4 NFE AF: 0.939

Gnomad4 OTH AF: 0.850

Alfa AF: 0.875 Hom.: 7368

Bravo AF: 0.809

Asia WGS AF: 0.843 AC: 2932 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.43
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1398193; hg19: chr18-45987139;