rs1866338

Variant names:

• chr18-78542601-G-A
• rs1866338

Your query was ambiguous. Multiple possible variants found:

• chr18-78542601-G-A
• chr18-78542601-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 0.39 in 152,116 control chromosomes in the GnomAD database, including 12,366 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 0.39 (12366 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.425

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.443 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: 0.390 AC: 59224 AN: 151998 Hom.: 12353 Cov.: 33

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.450

Gnomad ASJ AF: 0.387

Gnomad EAS AF: 0.427

Gnomad SAS AF: 0.326

Gnomad FIN AF: 0.499

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.447

Gnomad OTH AF: 0.386

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

GnomAD4 genome AF: 0.390 AC: 59260 AN: 152116 Hom.: 12366 Cov.: 33 AF XY: 0.390 AC XY: 29002 AN XY: 74356

Gnomad4 AFR AF: 0.248

Gnomad4 AMR AF: 0.450

Gnomad4 ASJ AF: 0.387

Gnomad4 EAS AF: 0.427

Gnomad4 SAS AF: 0.326

Gnomad4 FIN AF: 0.499

Gnomad4 NFE AF: 0.447

Gnomad4 OTH AF: 0.386

Alfa AF: 0.184 Hom.: 289

Bravo AF: 0.387

Asia WGS AF: 0.387 AC: 1347 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.3
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1866338; hg19: chr18-76302601;