18-66248779-G-T

Position:

• chr18-66248779-G-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 0.731 in 152,074 control chromosomes in the GnomAD database, including 41,143 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 0.73 (41143 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.114

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.879 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: 0.731 AC: 111137 AN: 151956 Hom.: 41099 Cov.: 32

Gnomad AFR AF: 0.819

Gnomad AMI AF: 0.689

Gnomad AMR AF: 0.627

Gnomad ASJ AF: 0.703

Gnomad EAS AF: 0.900

Gnomad SAS AF: 0.685

Gnomad FIN AF: 0.765

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.689

Gnomad OTH AF: 0.719

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

GnomAD4 genome AF: 0.731 AC: 111233 AN: 152074 Hom.: 41143 Cov.: 32 AF XY: 0.734 AC XY: 54574 AN XY: 74378

Gnomad4 AFR AF: 0.819

Gnomad4 AMR AF: 0.626

Gnomad4 ASJ AF: 0.703

Gnomad4 EAS AF: 0.900

Gnomad4 SAS AF: 0.685

Gnomad4 FIN AF: 0.765

Gnomad4 NFE AF: 0.689

Gnomad4 OTH AF: 0.722

Alfa AF: 0.692 Hom.: 38617

Bravo AF: 0.725

Asia WGS AF: 0.786 AC: 2727 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.9
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1115947; hg19: chr18-63916016;