rs17063905

chr18-57586872-T-C

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The variant allele was found at a frequency of 0.239 in 379,802 control chromosomes in the GnomAD database, including 12,912 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.28 (7034 hom., cov: 33)
  • Exomes 𝑓: 0.21 (5878 hom.)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.790

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BP6: Variant 18-57586872-T-C is Benign according to our data. Variant chr18-57586872-T-C is described in ClinVar as [Benign]. Clinvar id is 255310.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.448 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: 0.277 AC: 42063 AN: 152038 Hom.: 7017 Cov.: 33

Gnomad AFR AF: 0.453

Gnomad AMI AF: 0.0824

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.214

Gnomad EAS AF: 0.330

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.260

GnomAD4 exome AF: 0.213 AC: 48535 AN: 227646 Hom.: 5878 AF XY: 0.212 AC XY: 24844 AN XY: 117410

Gnomad4 AFR exome AF: 0.442

Gnomad4 AMR exome AF: 0.336

Gnomad4 ASJ exome AF: 0.224

Gnomad4 EAS exome AF: 0.404

Gnomad4 SAS exome AF: 0.245

Gnomad4 FIN exome AF: 0.234

Gnomad4 NFE exome AF: 0.171

Gnomad4 OTH exome AF: 0.213

GnomAD4 genome AF: 0.277 AC: 42141 AN: 152156 Hom.: 7034 Cov.: 33 AF XY: 0.280 AC XY: 20847 AN XY: 74396

Gnomad4 AFR AF: 0.453

Gnomad4 AMR AF: 0.302

Gnomad4 ASJ AF: 0.214

Gnomad4 EAS AF: 0.330

Gnomad4 SAS AF: 0.244

Gnomad4 FIN AF: 0.251

Gnomad4 NFE AF: 0.172

Gnomad4 OTH AF: 0.262

Alfa AF: 0.229 Hom.: 612

Bravo AF: 0.291

Asia WGS AF: 0.295 AC: 1025 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not specified Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

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- -

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 11, 2018

This variant is associated with the following publications: (PMID: 15850836) -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	4.0
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17063905; hg19: chr18-55254104;