rs1557351

chr18-57085083-T-C

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 0.253 in 152,132 control chromosomes in the GnomAD database, including 5,054 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 0.25 (5054 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.403

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.385 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: 0.252 AC: 38372 AN: 152012 Hom.: 5035 Cov.: 33

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.330

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.399

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.253 AC: 38439 AN: 152132 Hom.: 5054 Cov.: 33 AF XY: 0.259 AC XY: 19244 AN XY: 74384

Gnomad4 AFR AF: 0.264

Gnomad4 AMR AF: 0.331

Gnomad4 ASJ AF: 0.268

Gnomad4 EAS AF: 0.399

Gnomad4 SAS AF: 0.238

Gnomad4 FIN AF: 0.278

Gnomad4 NFE AF: 0.214

Gnomad4 OTH AF: 0.267

Alfa AF: 0.230 Hom.: 9654

Bravo AF: 0.262

Asia WGS AF: 0.335 AC: 1168 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	7.2
Dann	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1557351; hg19: chr18-54752314;