chr18-60183189-G-T

Variant names:

• chr18-60183189-G-T
• rs538656

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 0.268 in 151,870 control chromosomes in the GnomAD database, including 5,976 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 0.27 (5976 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.567
• Publications: 39 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.383 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.268 AC: 40657 AN: 151752 Hom.: 5962 Cov.: 32

Gnomad AFR AF: 0.388

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.183

Gnomad SAS AF: 0.350

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.235

Gnomad OTH AF: 0.246

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

GnomAD4 genome AF: 0.268 AC: 40715 AN: 151870 Hom.: 5976 Cov.: 32 AF XY: 0.264 AC XY: 19597 AN XY: 74278

African (AFR) AF: 0.388 AC: 16060 AN: 41396

American (AMR) AF: 0.170 AC: 2591 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.215 AC: 746 AN: 3472

East Asian (EAS) AF: 0.183 AC: 946 AN: 5178

South Asian (SAS) AF: 0.351 AC: 1692 AN: 4814

European-Finnish (FIN) AF: 0.172 AC: 1806 AN: 10530

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.235 AC: 15988 AN: 67926

Other (OTH) AF: 0.246 AC: 519 AN: 2110

Alfa AF: 0.256 Hom.: 1566

Bravo AF: 0.271

Asia WGS AF: 0.233 AC: 802 AN: 3436

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.6
DANN	Benign	0.39
PhyloP100		0.57

Splicing

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

Other links and lift over

dbSNP: rs538656; hg19: chr18-57850422;