18-60228805-G-T

Variant names:

• chr18-60228805-G-T
• rs477181

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 0.376 in 151,944 control chromosomes in the GnomAD database, including 11,506 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 0.38 (11506 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.533
• Publications: 17 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.513 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.375 AC: 56986 AN: 151826 Hom.: 11477 Cov.: 32

Gnomad AFR AF: 0.518

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.288

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.472

Gnomad FIN AF: 0.326

Gnomad MID AF: 0.404

Gnomad NFE AF: 0.337

Gnomad OTH AF: 0.342

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

GnomAD4 genome AF: 0.376 AC: 57055 AN: 151944 Hom.: 11506 Cov.: 32 AF XY: 0.373 AC XY: 27682 AN XY: 74266

African (AFR) AF: 0.518 AC: 21485 AN: 41440

American (AMR) AF: 0.250 AC: 3814 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.288 AC: 998 AN: 3462

East Asian (EAS) AF: 0.188 AC: 970 AN: 5164

South Asian (SAS) AF: 0.472 AC: 2266 AN: 4798

European-Finnish (FIN) AF: 0.326 AC: 3443 AN: 10562

Middle Eastern (MID) AF: 0.401 AC: 117 AN: 292

European-Non Finnish (NFE) AF: 0.337 AC: 22871 AN: 67938

Other (OTH) AF: 0.342 AC: 724 AN: 2116

Alfa AF: 0.343 Hom.: 28543

Bravo AF: 0.373

Asia WGS AF: 0.307 AC: 1068 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.13
DANN	Benign	0.55
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs477181; hg19: chr18-57896038;