18-60350016-T-C

Position:

• chr18-60350016-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 0.631 in 151,942 control chromosomes in the GnomAD database, including 31,523 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 0.63 (31523 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.505

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.878 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.60350016T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000285681	ENST00000650201.1	n.113+20671T>C		intron_variant
ENSG00000285681	ENST00000658928.1	n.156+20671T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.631 AC: 95780 AN: 151824 Hom.: 31507 Cov.: 31

Gnomad AFR AF: 0.434

Gnomad AMI AF: 0.720

Gnomad AMR AF: 0.712

Gnomad ASJ AF: 0.763

Gnomad EAS AF: 0.900

Gnomad SAS AF: 0.670

Gnomad FIN AF: 0.729

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.684

Gnomad OTH AF: 0.674

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

GnomAD4 genome AF: 0.631 AC: 95829 AN: 151942 Hom.: 31523 Cov.: 31 AF XY: 0.641 AC XY: 47613 AN XY: 74270

Gnomad4 AFR AF: 0.434

Gnomad4 AMR AF: 0.713

Gnomad4 ASJ AF: 0.763

Gnomad4 EAS AF: 0.900

Gnomad4 SAS AF: 0.670

Gnomad4 FIN AF: 0.729

Gnomad4 NFE AF: 0.684

Gnomad4 OTH AF: 0.676

Alfa AF: 0.681 Hom.: 46688

Bravo AF: 0.618

Asia WGS AF: 0.773 AC: 2689 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.45
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11152221; hg19: chr18-58017249;