rs538656

chr18-60183189-G-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;