rs538656

Variant names:

• chr18-60183189-G-T
• rs538656

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 0.268 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.268 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

Gnomad4 AFR AF: 0.388

Gnomad4 AMR AF: 0.170

Gnomad4 ASJ AF: 0.215

Gnomad4 EAS AF: 0.183

Gnomad4 SAS AF: 0.351

Gnomad4 FIN AF: 0.172

Gnomad4 NFE AF: 0.235

Gnomad4 OTH AF: 0.246

Alfa AF: 0.247 Hom.: 641

Bravo AF: 0.271

Asia WGS AF: 0.233 AC: 802 AN: 3436

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs538656; hg19: chr18-57850422;