chr18-78897779-C-T

Variant names:

• chr18-78897779-C-T
• rs9951602

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 0.156 in 152,134 control chromosomes in the GnomAD database, including 2,159 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 0.16 (2159 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.763
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.346 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: 0.156 AC: 23649 AN: 152016 Hom.: 2158 Cov.: 33

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.359

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.156 AC: 23662 AN: 152134 Hom.: 2159 Cov.: 33 AF XY: 0.161 AC XY: 12006 AN XY: 74356

African (AFR) AF: 0.100 AC: 4171 AN: 41530

American (AMR) AF: 0.203 AC: 3109 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.129 AC: 449 AN: 3470

East Asian (EAS) AF: 0.359 AC: 1857 AN: 5166

South Asian (SAS) AF: 0.331 AC: 1591 AN: 4812

European-Finnish (FIN) AF: 0.195 AC: 2060 AN: 10566

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.146 AC: 9894 AN: 67986

Other (OTH) AF: 0.150 AC: 317 AN: 2110

Alfa AF: 0.147 Hom.: 4676

Bravo AF: 0.152

Asia WGS AF: 0.333 AC: 1158 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.3
DANN	Benign	0.63
PhyloP100		0.76

Splicing

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

Other links and lift over

dbSNP: rs9951602; hg19: chr18-76657779;