18-78155097-C-T

Variant names:

• chr18-78155097-C-T
• rs10468814

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 0.39 in 151,764 control chromosomes in the GnomAD database, including 11,823 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 0.39 (11823 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.614 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: 0.390 AC: 59141 AN: 151646 Hom.: 11818 Cov.: 32

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.444

Gnomad ASJ AF: 0.330

Gnomad EAS AF: 0.632

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.433

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.389

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.390 AC: 59186 AN: 151764 Hom.: 11823 Cov.: 32 AF XY: 0.392 AC XY: 29109 AN XY: 74190

African (AFR) AF: 0.348 AC: 14373 AN: 41276

American (AMR) AF: 0.443 AC: 6776 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.330 AC: 1146 AN: 3470

East Asian (EAS) AF: 0.632 AC: 3232 AN: 5114

South Asian (SAS) AF: 0.294 AC: 1415 AN: 4820

European-Finnish (FIN) AF: 0.433 AC: 4571 AN: 10558

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.389 AC: 26395 AN: 67928

Other (OTH) AF: 0.371 AC: 783 AN: 2110

Alfa AF: 0.389 Hom.: 18602

Bravo AF: 0.398

Asia WGS AF: 0.475 AC: 1653 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.27
DANN	Benign	0.69
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs10468814; hg19: chr18-75915097;