chr18-4487509-C-T

Variant names:

• chr18-4487509-C-T
• rs1395204

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 0.455 in 138,890 control chromosomes in the GnomAD database, including 13,457 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 0.45 (13457 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.194

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.584 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: 0.455 AC: 63075 AN: 138764 Hom.: 13437 Cov.: 27

Gnomad AFR AF: 0.590

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.317

Gnomad FIN AF: 0.514

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.404

Gnomad OTH AF: 0.396

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

GnomAD4 genome AF: 0.455 AC: 63146 AN: 138890 Hom.: 13457 Cov.: 27 AF XY: 0.455 AC XY: 30825 AN XY: 67694

Gnomad4 AFR AF: 0.590

Gnomad4 AMR AF: 0.350

Gnomad4 ASJ AF: 0.329

Gnomad4 EAS AF: 0.389

Gnomad4 SAS AF: 0.316

Gnomad4 FIN AF: 0.514

Gnomad4 NFE AF: 0.404

Gnomad4 OTH AF: 0.404

Alfa AF: 0.330 Hom.: 1874

Bravo AF: 0.425

Asia WGS AF: 0.368 AC: 1273 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.0
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1395204; hg19: chr18-4487509;