rs1557351

Variant names:

• chr18-57085083-T-C
• rs1557351

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;