18-66248779-G-T

Variant names:

• chr18-66248779-G-T
• rs1115947

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;