chr18-73854856-T-G

Position:

• chr18-73854856-T-G

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 0.103 in 152,186 control chromosomes in the GnomAD database, including 1,122 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 0.10 (1122 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.22

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.191 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: 0.103 AC: 15658 AN: 152068 Hom.: 1119 Cov.: 32

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.0404

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.0222

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0523

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.103 AC: 15681 AN: 152186 Hom.: 1122 Cov.: 32 AF XY: 0.104 AC XY: 7727 AN XY: 74420

Gnomad4 AFR AF: 0.195

Gnomad4 AMR AF: 0.128

Gnomad4 ASJ AF: 0.0404

Gnomad4 EAS AF: 0.163

Gnomad4 SAS AF: 0.109

Gnomad4 FIN AF: 0.0222

Gnomad4 NFE AF: 0.0523

Gnomad4 OTH AF: 0.0992

Alfa AF: 0.0624 Hom.: 406

Bravo AF: 0.113

Asia WGS AF: 0.145 AC: 503 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.17
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17088439; hg19: chr18-71522091;