rs1799809

Positions:

• chr2-127418299-G-A
• chr2-127418299-G-C
• chr2-127418299-G-T

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 0.578 in 616,284 control chromosomes in the GnomAD database, including 106,407 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.52 (22574 hom., cov: 31)
  • Exomes 𝑓: 0.60 (83833 hom.)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.0500

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BP6: Variant 2-127418299-G-A is Benign according to our data. Variant chr2-127418299-G-A is described in ClinVar as [Benign]. Clinvar id is 1164170.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.804 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.524 AC: 79674 AN: 151916 Hom.: 22554 Cov.: 31

Gnomad AFR AF: 0.312

Gnomad AMI AF: 0.517

Gnomad AMR AF: 0.659

Gnomad ASJ AF: 0.502

Gnomad EAS AF: 0.824

Gnomad SAS AF: 0.579

Gnomad FIN AF: 0.660

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.577

Gnomad OTH AF: 0.535

GnomAD4 exome AF: 0.596 AC: 276547 AN: 464248 Hom.: 83833 AF XY: 0.594 AC XY: 142355 AN XY: 239712

Gnomad4 AFR exome AF: 0.312

Gnomad4 AMR exome AF: 0.753

Gnomad4 ASJ exome AF: 0.521

Gnomad4 EAS exome AF: 0.832

Gnomad4 SAS exome AF: 0.570

Gnomad4 FIN exome AF: 0.649

Gnomad4 NFE exome AF: 0.592

Gnomad4 OTH exome AF: 0.590

GnomAD4 genome AF: 0.524 AC: 79727 AN: 152036 Hom.: 22574 Cov.: 31 AF XY: 0.534 AC XY: 39689 AN XY: 74308

Gnomad4 AFR AF: 0.312

Gnomad4 AMR AF: 0.659

Gnomad4 ASJ AF: 0.502

Gnomad4 EAS AF: 0.824

Gnomad4 SAS AF: 0.578

Gnomad4 FIN AF: 0.660

Gnomad4 NFE AF: 0.577

Gnomad4 OTH AF: 0.539

Alfa AF: 0.573 Hom.: 42279

Bravo AF: 0.518

Asia WGS AF: 0.719 AC: 2497 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Thrombophilia due to protein C deficiency, autosomal dominant Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 18, 2024

- -

not provided Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

-

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	7.0
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1799809; hg19: chr2-128175875;