18-60441957-C-T

Position:

• chr18-60441957-C-T

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 0.709 in 152,110 control chromosomes in the GnomAD database, including 39,737 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 0.71 (39737 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.279

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.931 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.60441957C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000285681	ENST00000650201.1	n.114-37614C>T		intron_variant
ENSG00000285681	ENST00000658928.1	n.157-37614C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.709 AC: 107771 AN: 151992 Hom.: 39691 Cov.: 32

Gnomad AFR AF: 0.896

Gnomad AMI AF: 0.529

Gnomad AMR AF: 0.672

Gnomad ASJ AF: 0.568

Gnomad EAS AF: 0.953

Gnomad SAS AF: 0.682

Gnomad FIN AF: 0.594

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.615

Gnomad OTH AF: 0.684

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

GnomAD4 genome AF: 0.709 AC: 107875 AN: 152110 Hom.: 39737 Cov.: 32 AF XY: 0.710 AC XY: 52799 AN XY: 74332

Gnomad4 AFR AF: 0.896

Gnomad4 AMR AF: 0.672

Gnomad4 ASJ AF: 0.568

Gnomad4 EAS AF: 0.953

Gnomad4 SAS AF: 0.682

Gnomad4 FIN AF: 0.594

Gnomad4 NFE AF: 0.615

Gnomad4 OTH AF: 0.684

Alfa AF: 0.632 Hom.: 37969

Bravo AF: 0.725

Asia WGS AF: 0.848 AC: 2949 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	2.5
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4257308; hg19: chr18-58109190;