18-78299948-T-C

Variant names:

• chr18-78299948-T-C
• rs626549

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 0.813 in 151,638 control chromosomes in the GnomAD database, including 51,036 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 0.81 (51036 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.89 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: 0.813 AC: 123180 AN: 151520 Hom.: 51000 Cov.: 28

Gnomad AFR AF: 0.642

Gnomad AMI AF: 0.872

Gnomad AMR AF: 0.812

Gnomad ASJ AF: 0.950

Gnomad EAS AF: 0.790

Gnomad SAS AF: 0.829

Gnomad FIN AF: 0.895

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.896

Gnomad OTH AF: 0.828

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

GnomAD4 genome AF: 0.813 AC: 123268 AN: 151638 Hom.: 51036 Cov.: 28 AF XY: 0.816 AC XY: 60452 AN XY: 74092

African (AFR) AF: 0.642 AC: 26504 AN: 41266

American (AMR) AF: 0.812 AC: 12363 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.950 AC: 3298 AN: 3472

East Asian (EAS) AF: 0.790 AC: 4039 AN: 5114

South Asian (SAS) AF: 0.829 AC: 3975 AN: 4794

European-Finnish (FIN) AF: 0.895 AC: 9421 AN: 10526

Middle Eastern (MID) AF: 0.918 AC: 270 AN: 294

European-Non Finnish (NFE) AF: 0.896 AC: 60865 AN: 67932

Other (OTH) AF: 0.824 AC: 1738 AN: 2108

Alfa AF: 0.851 Hom.: 23425

Bravo AF: 0.797

Asia WGS AF: 0.783 AC: 2728 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.022
DANN	Benign	0.66
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs626549; hg19: chr18-76059948;