chr18-60087885-C-T

Variant names:

• chr18-60087885-C-T
• rs6567155

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 0.3 in 152,044 control chromosomes in the GnomAD database, including 7,708 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 0.30 (7708 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0770

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.456 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45484 AN: 151926 Hom.: 7693 Cov.: 33

Gnomad AFR AF: 0.461

Gnomad AMI AF: 0.299

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.251

Gnomad OTH AF: 0.294

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

GnomAD4 genome AF: 0.300 AC: 45549 AN: 152044 Hom.: 7708 Cov.: 33 AF XY: 0.294 AC XY: 21874 AN XY: 74308

Gnomad4 AFR AF: 0.461

Gnomad4 AMR AF: 0.200

Gnomad4 ASJ AF: 0.254

Gnomad4 EAS AF: 0.170

Gnomad4 SAS AF: 0.344

Gnomad4 FIN AF: 0.176

Gnomad4 NFE AF: 0.251

Gnomad4 OTH AF: 0.294

Alfa AF: 0.260 Hom.: 7102

Bravo AF: 0.306

Asia WGS AF: 0.224 AC: 775 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.4
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6567155; hg19: chr18-57755117;