18-75815681-C-T

Position:

• chr18-75815681-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 0.563 in 151,946 control chromosomes in the GnomAD database, including 24,979 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 0.56 (24979 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.370

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.775 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.563 AC: 85491 AN: 151826 Hom.: 24956 Cov.: 32

Gnomad AFR AF: 0.425

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.651

Gnomad ASJ AF: 0.576

Gnomad EAS AF: 0.795

Gnomad SAS AF: 0.706

Gnomad FIN AF: 0.666

Gnomad MID AF: 0.599

Gnomad NFE AF: 0.585

Gnomad OTH AF: 0.576

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

GnomAD4 genome AF: 0.563 AC: 85549 AN: 151946 Hom.: 24979 Cov.: 32 AF XY: 0.572 AC XY: 42451 AN XY: 74276

Gnomad4 AFR AF: 0.425

Gnomad4 AMR AF: 0.651

Gnomad4 ASJ AF: 0.576

Gnomad4 EAS AF: 0.795

Gnomad4 SAS AF: 0.705

Gnomad4 FIN AF: 0.666

Gnomad4 NFE AF: 0.585

Gnomad4 OTH AF: 0.583

Alfa AF: 0.588 Hom.: 28275

Bravo AF: 0.557

Asia WGS AF: 0.726 AC: 2518 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.5
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1017745; hg19: chr18-73527636;