18-1604959-T-C

Position:

• chr18-1604959-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 0.376 in 151,914 control chromosomes in the GnomAD database, including 11,659 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 0.38 (11659 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.130

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.714 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.1604959T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000266602	ENST00000583163.2	n.336-21280T>C		intron_variant		2
ENSG00000266602	ENST00000652957.1	n.251+38435T>C		intron_variant
ENSG00000266602	ENST00000653006.1	n.312-21280T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.376 AC: 57075 AN: 151796 Hom.: 11638 Cov.: 31

Gnomad AFR AF: 0.473

Gnomad AMI AF: 0.554

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.316

Gnomad EAS AF: 0.733

Gnomad SAS AF: 0.519

Gnomad FIN AF: 0.323

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.379

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

GnomAD4 genome AF: 0.376 AC: 57144 AN: 151914 Hom.: 11659 Cov.: 31 AF XY: 0.383 AC XY: 28435 AN XY: 74256

Gnomad4 AFR AF: 0.473

Gnomad4 AMR AF: 0.386

Gnomad4 ASJ AF: 0.316

Gnomad4 EAS AF: 0.733

Gnomad4 SAS AF: 0.520

Gnomad4 FIN AF: 0.323

Gnomad4 NFE AF: 0.287

Gnomad4 OTH AF: 0.381

Alfa AF: 0.301 Hom.: 7217

Bravo AF: 0.386

Asia WGS AF: 0.606 AC: 2107 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.4
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12604976; hg19: chr18-1604960;