18-60350208-T-C

Position:

• chr18-60350208-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 0.0283 in 152,012 control chromosomes in the GnomAD database, including 125 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 0.028 (125 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0737 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.60350208T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000285681	ENST00000650201.1	n.113+20863T>C		intron_variant
ENSG00000285681	ENST00000658928.1	n.156+20863T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0283 AC: 4292 AN: 151894 Hom.: 125 Cov.: 32

Gnomad AFR AF: 0.0759

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0125

Gnomad ASJ AF: 0.00778

Gnomad EAS AF: 0.00464

Gnomad SAS AF: 0.00646

Gnomad FIN AF: 0.00123

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0119

Gnomad OTH AF: 0.0239

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

GnomAD4 genome AF: 0.0283 AC: 4301 AN: 152012 Hom.: 125 Cov.: 32 AF XY: 0.0268 AC XY: 1988 AN XY: 74304

Gnomad4 AFR AF: 0.0759

Gnomad4 AMR AF: 0.0125

Gnomad4 ASJ AF: 0.00778

Gnomad4 EAS AF: 0.00465

Gnomad4 SAS AF: 0.00667

Gnomad4 FIN AF: 0.00123

Gnomad4 NFE AF: 0.0119

Gnomad4 OTH AF: 0.0232

Alfa AF: 0.00149 Hom.: 0

Bravo AF: 0.0326

Asia WGS AF: 0.0150 AC: 53 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	4.3
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs72973926; hg19: chr18-58017441;