chr18-60101295-T-G

Variant names:

• chr18-60101295-T-G
• rs17066582

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 0.0821 in 152,098 control chromosomes in the GnomAD database, including 530 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 0.082 (530 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.02
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.103 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: 0.0821 AC: 12472 AN: 151980 Hom.: 528 Cov.: 32

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.0968

Gnomad ASJ AF: 0.0141

Gnomad EAS AF: 0.0129

Gnomad SAS AF: 0.0306

Gnomad FIN AF: 0.0885

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0769

Gnomad OTH AF: 0.0726

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

GnomAD4 genome AF: 0.0821 AC: 12483 AN: 152098 Hom.: 530 Cov.: 32 AF XY: 0.0810 AC XY: 6023 AN XY: 74364

African (AFR) AF: 0.106 AC: 4400 AN: 41490

American (AMR) AF: 0.0966 AC: 1472 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.0141 AC: 49 AN: 3466

East Asian (EAS) AF: 0.0131 AC: 68 AN: 5178

South Asian (SAS) AF: 0.0304 AC: 147 AN: 4830

European-Finnish (FIN) AF: 0.0885 AC: 937 AN: 10586

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0769 AC: 5225 AN: 67982

Other (OTH) AF: 0.0714 AC: 151 AN: 2116

Alfa AF: 0.0766 Hom.: 362

Bravo AF: 0.0833

Asia WGS AF: 0.0270 AC: 93 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	7.7
DANN	Benign	0.68
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs17066582; hg19: chr18-57768527;