chr18-77145362-C-T

Variant names:

• chr18-77145362-C-T
• rs9951586

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;