chr18-77145362-C-T

Position:

• chr18-77145362-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.688 in 152,168 control chromosomes in the GnomAD database, including 37,595 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 0.69 (37595 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305

ACMG classification

Verdict is Benign. Variant got -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 = 0.795 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.688 AC: 104573 AN: 152050 Hom.: 37568 Cov.: 33

Gnomad AFR AF: 0.463

Gnomad AMI AF: 0.808

Gnomad AMR AF: 0.738

Gnomad ASJ AF: 0.666

Gnomad EAS AF: 0.737

Gnomad SAS AF: 0.604

Gnomad FIN AF: 0.779

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.801

Gnomad OTH AF: 0.691

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

GnomAD4 genome AF: 0.688 AC: 104655 AN: 152168 Hom.: 37595 Cov.: 33 AF XY: 0.688 AC XY: 51172 AN XY: 74382

Gnomad4 AFR AF: 0.463

Gnomad4 AMR AF: 0.738

Gnomad4 ASJ AF: 0.666

Gnomad4 EAS AF: 0.738

Gnomad4 SAS AF: 0.604

Gnomad4 FIN AF: 0.779

Gnomad4 NFE AF: 0.801

Gnomad4 OTH AF: 0.695

Alfa AF: 0.774 Hom.: 91232

Bravo AF: 0.674

Asia WGS AF: 0.621 AC: 2160 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.1
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9951586; hg19: chr18-74857318;