18-59955055-T-C

Position:

• chr18-59955055-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 0.672 in 152,154 control chromosomes in the GnomAD database, including 34,540 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 0.67 (34540 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.369

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.693 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.672 AC: 102189 AN: 152036 Hom.: 34516 Cov.: 33

Gnomad AFR AF: 0.677

Gnomad AMI AF: 0.799

Gnomad AMR AF: 0.649

Gnomad ASJ AF: 0.751

Gnomad EAS AF: 0.712

Gnomad SAS AF: 0.604

Gnomad FIN AF: 0.573

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.684

Gnomad OTH AF: 0.700

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

GnomAD4 genome AF: 0.672 AC: 102251 AN: 152154 Hom.: 34540 Cov.: 33 AF XY: 0.666 AC XY: 49545 AN XY: 74388

Gnomad4 AFR AF: 0.677

Gnomad4 AMR AF: 0.649

Gnomad4 ASJ AF: 0.751

Gnomad4 EAS AF: 0.712

Gnomad4 SAS AF: 0.605

Gnomad4 FIN AF: 0.573

Gnomad4 NFE AF: 0.684

Gnomad4 OTH AF: 0.693

Alfa AF: 0.686 Hom.: 60366

Bravo AF: 0.679

Asia WGS AF: 0.658 AC: 2290 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.4
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4368253; hg19: chr18-57622287;