chr18-77240802-T-C

Position:

• chr18-77240802-T-C

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 0.136 in 152,246 control chromosomes in the GnomAD database, including 1,567 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 0.14 (1567 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.662

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.166 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.136 AC: 20715 AN: 152128 Hom.: 1570 Cov.: 32

Gnomad AFR AF: 0.0925

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.136 AC: 20714 AN: 152246 Hom.: 1567 Cov.: 32 AF XY: 0.137 AC XY: 10191 AN XY: 74416

Gnomad4 AFR AF: 0.0926

Gnomad4 AMR AF: 0.118

Gnomad4 ASJ AF: 0.167

Gnomad4 EAS AF: 0.00154

Gnomad4 SAS AF: 0.176

Gnomad4 FIN AF: 0.193

Gnomad4 NFE AF: 0.164

Gnomad4 OTH AF: 0.135

Alfa AF: 0.160 Hom.: 2596

Bravo AF: 0.128

Asia WGS AF: 0.0750 AC: 262 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	7.5
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8084125; hg19: chr18-74952758;