rs6567155

Variant names:

• chr18-60087885-C-T
• rs6567155

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 10 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.461 AC: 19135 AN: 41476

American (AMR) AF: 0.200 AC: 3059 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.254 AC: 882 AN: 3468

East Asian (EAS) AF: 0.170 AC: 881 AN: 5186

South Asian (SAS) AF: 0.344 AC: 1656 AN: 4820

European-Finnish (FIN) AF: 0.176 AC: 1856 AN: 10548

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.251 AC: 17087 AN: 67954

Other (OTH) AF: 0.294 AC: 620 AN: 2112

Alfa AF: 0.271 Hom.: 9944

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
PhyloP100		-0.077

Splicing

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

Other links and lift over

dbSNP: rs6567155; hg19: chr18-57755117;