18-59955055-T-C

Variant names:

• chr18-59955055-T-C
• rs4368253

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 26 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.677 AC: 28092 AN: 41496

American (AMR) AF: 0.649 AC: 9918 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.751 AC: 2605 AN: 3470

East Asian (EAS) AF: 0.712 AC: 3686 AN: 5178

South Asian (SAS) AF: 0.605 AC: 2919 AN: 4824

European-Finnish (FIN) AF: 0.573 AC: 6064 AN: 10578

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.684 AC: 46536 AN: 67998

Other (OTH) AF: 0.693 AC: 1466 AN: 2114

Alfa AF: 0.684 Hom.: 141864

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
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs4368253; hg19: chr18-57622287;