8-18419609-C-T

Variant names:

• chr8-18419609-C-T
• rs1466753

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 0.429 in 151,996 control chromosomes in the GnomAD database, including 14,395 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 0.43 (14395 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.234

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 (NFE) allele frequency at 95% confidence interval = 0.462 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: 0.429 AC: 65209 AN: 151878 Hom.: 14386 Cov.: 32

Gnomad AFR AF: 0.367

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.440

Gnomad ASJ AF: 0.475

Gnomad EAS AF: 0.251

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.503

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.466

Gnomad OTH AF: 0.446

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

GnomAD4 genome AF: 0.429 AC: 65251 AN: 151996 Hom.: 14395 Cov.: 32 AF XY: 0.430 AC XY: 31948 AN XY: 74294

Gnomad4 AFR AF: 0.367

Gnomad4 AMR AF: 0.441

Gnomad4 ASJ AF: 0.475

Gnomad4 EAS AF: 0.251

Gnomad4 SAS AF: 0.406

Gnomad4 FIN AF: 0.503

Gnomad4 NFE AF: 0.466

Gnomad4 OTH AF: 0.446

Alfa AF: 0.440 Hom.: 6588

Bravo AF: 0.423

Asia WGS AF: 0.323 AC: 1123 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	3.1
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1466753; hg19: chr8-18277119;