rs782584

chr2-55693981-C-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The variant allele was found at a frequency of 0.455 in 847,598 control chromosomes in the GnomAD database, including 92,453 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.44 (15474 hom., cov: 33)
  • Exomes 𝑓: 0.46 (76979 hom.)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.814

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BP6: Variant 2-55693981-C-G is Benign according to our data. Variant chr2-55693981-C-G is described in ClinVar as [Benign]. Clinvar id is 1241660.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.502 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: 0.438 AC: 66597 AN: 151988 Hom.: 15477 Cov.: 33

Gnomad AFR AF: 0.335

Gnomad AMI AF: 0.305

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.475

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.566

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.507

Gnomad OTH AF: 0.462

GnomAD4 exome AF: 0.458 AC: 318835 AN: 695492 Hom.: 76979 AF XY: 0.452 AC XY: 159614 AN XY: 353202

Gnomad4 AFR exome AF: 0.325

Gnomad4 AMR exome AF: 0.468

Gnomad4 ASJ exome AF: 0.479

Gnomad4 EAS exome AF: 0.121

Gnomad4 SAS exome AF: 0.269

Gnomad4 FIN exome AF: 0.556

Gnomad4 NFE exome AF: 0.499

Gnomad4 OTH exome AF: 0.452

GnomAD4 genome AF: 0.438 AC: 66615 AN: 152106 Hom.: 15474 Cov.: 33 AF XY: 0.436 AC XY: 32414 AN XY: 74372

Gnomad4 AFR AF: 0.334

Gnomad4 AMR AF: 0.489

Gnomad4 ASJ AF: 0.475

Gnomad4 EAS AF: 0.110

Gnomad4 SAS AF: 0.258

Gnomad4 FIN AF: 0.566

Gnomad4 NFE AF: 0.507

Gnomad4 OTH AF: 0.459

Alfa AF: 0.474 Hom.: 2144

Bravo AF: 0.428

Asia WGS AF: 0.231 AC: 805 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 23, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	1.6
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs782584; hg19: chr2-55921116;