18-78325495-C-T

Variant names:

• chr18-78325495-C-T
• rs592629

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 0.7 in 151,992 control chromosomes in the GnomAD database, including 40,418 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 0.70 (40418 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.64
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.864 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: 0.700 AC: 106314 AN: 151874 Hom.: 40422 Cov.: 32

Gnomad AFR AF: 0.370

Gnomad AMI AF: 0.759

Gnomad AMR AF: 0.820

Gnomad ASJ AF: 0.842

Gnomad EAS AF: 0.885

Gnomad SAS AF: 0.787

Gnomad FIN AF: 0.829

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.823

Gnomad OTH AF: 0.733

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

GnomAD4 genome AF: 0.700 AC: 106337 AN: 151992 Hom.: 40418 Cov.: 32 AF XY: 0.708 AC XY: 52621 AN XY: 74286

African (AFR) AF: 0.370 AC: 15311 AN: 41400

American (AMR) AF: 0.821 AC: 12546 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.842 AC: 2921 AN: 3468

East Asian (EAS) AF: 0.886 AC: 4557 AN: 5146

South Asian (SAS) AF: 0.787 AC: 3793 AN: 4818

European-Finnish (FIN) AF: 0.829 AC: 8784 AN: 10596

Middle Eastern (MID) AF: 0.786 AC: 231 AN: 294

European-Non Finnish (NFE) AF: 0.823 AC: 55960 AN: 67966

Other (OTH) AF: 0.732 AC: 1545 AN: 2112

Alfa AF: 0.790 Hom.: 21040

Bravo AF: 0.685

Asia WGS AF: 0.798 AC: 2776 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.25
DANN	Benign	0.46
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs592629; hg19: chr18-76085495;