18-63098869-T-C

Position:

• chr18-63098869-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 0.762 in 152,100 control chromosomes in the GnomAD database, including 44,440 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 0.76 (44440 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.03

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.833 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.63098869T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.762 AC: 115828 AN: 151984 Hom.: 44368 Cov.: 31

Gnomad AFR AF: 0.839

Gnomad AMI AF: 0.869

Gnomad AMR AF: 0.762

Gnomad ASJ AF: 0.792

Gnomad EAS AF: 0.786

Gnomad SAS AF: 0.740

Gnomad FIN AF: 0.715

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.720

Gnomad OTH AF: 0.735

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

GnomAD4 genome AF: 0.762 AC: 115959 AN: 152100 Hom.: 44440 Cov.: 31 AF XY: 0.759 AC XY: 56459 AN XY: 74346

Gnomad4 AFR AF: 0.840

Gnomad4 AMR AF: 0.762

Gnomad4 ASJ AF: 0.792

Gnomad4 EAS AF: 0.786

Gnomad4 SAS AF: 0.740

Gnomad4 FIN AF: 0.715

Gnomad4 NFE AF: 0.720

Gnomad4 OTH AF: 0.739

Alfa AF: 0.720 Hom.: 34999

Bravo AF: 0.770

Asia WGS AF: 0.749 AC: 2604 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.014
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8083921; hg19: chr18-60766102;