8-18419609-C-T

Variant names:

• chr8-18419609-C-T
• rs1466753

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.367 AC: 15192 AN: 41420

American (AMR) AF: 0.441 AC: 6727 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.475 AC: 1646 AN: 3468

East Asian (EAS) AF: 0.251 AC: 1300 AN: 5176

South Asian (SAS) AF: 0.406 AC: 1959 AN: 4824

European-Finnish (FIN) AF: 0.503 AC: 5306 AN: 10554

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.466 AC: 31695 AN: 67966

Other (OTH) AF: 0.446 AC: 943 AN: 2114

Alfa AF: 0.442 Hom.: 7510

Bravo AF: 0.423

Asia WGS AF: 0.323 AC: 1123 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.1
DANN	Benign	0.88
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs1466753; hg19: chr8-18277119;