chr18-21113636-G-T

Variant names:

• chr18-21113636-G-T
• rs8089974

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 0.804 in 151,920 control chromosomes in the GnomAD database, including 52,999 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 0.80 (52999 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.112

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 (SAS) allele frequency at 95% confidence interval = 0.959 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: 0.804 AC: 122096 AN: 151804 Hom.: 53010 Cov.: 30

Gnomad AFR AF: 0.444

Gnomad AMI AF: 0.986

Gnomad AMR AF: 0.808

Gnomad ASJ AF: 0.927

Gnomad EAS AF: 0.912

Gnomad SAS AF: 0.966

Gnomad FIN AF: 0.977

Gnomad MID AF: 0.883

Gnomad NFE AF: 0.965

Gnomad OTH AF: 0.835

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

GnomAD4 genome AF: 0.804 AC: 122115 AN: 151920 Hom.: 52999 Cov.: 30 AF XY: 0.807 AC XY: 59968 AN XY: 74270

Gnomad4 AFR AF: 0.444

Gnomad4 AMR AF: 0.807

Gnomad4 ASJ AF: 0.927

Gnomad4 EAS AF: 0.912

Gnomad4 SAS AF: 0.965

Gnomad4 FIN AF: 0.977

Gnomad4 NFE AF: 0.965

Gnomad4 OTH AF: 0.835

Alfa AF: 0.873 Hom.: 7563

Bravo AF: 0.773

Asia WGS AF: 0.895 AC: 3108 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.5
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: rs8089974; hg19: chr18-18693597;