18-63098869-T-C

Variant names:

• chr18-63098869-T-C
• rs8083921

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.03

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;