rs1876487

Positions:

• chr2-72887223-A-C
• chr2-72887223-A-G
• chr2-72887223-A-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 0.654 in 462,886 control chromosomes in the GnomAD database, including 107,537 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.55 (28196 hom., cov: 33)
  • Exomes 𝑓: 0.70 (79341 hom.)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:3
• Conservation: PhyloP100: -5.97

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BP6: Variant 2-72887223-A-C is Benign according to our data. Variant chr2-72887223-A-C is described in ClinVar as [Benign]. Clinvar id is 1167479.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.912 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: 0.552 AC: 83872 AN: 151992 Hom.: 28209 Cov.: 33

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.630

Gnomad AMR AF: 0.590

Gnomad ASJ AF: 0.763

Gnomad EAS AF: 0.934

Gnomad SAS AF: 0.851

Gnomad FIN AF: 0.730

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.697

Gnomad OTH AF: 0.587

GnomAD4 exome AF: 0.704 AC: 218778 AN: 310778 Hom.: 79341 AF XY: 0.709 AC XY: 112273 AN XY: 158430

Gnomad4 AFR exome AF: 0.147

Gnomad4 AMR exome AF: 0.607

Gnomad4 ASJ exome AF: 0.760

Gnomad4 EAS exome AF: 0.932

Gnomad4 SAS exome AF: 0.839

Gnomad4 FIN exome AF: 0.717

Gnomad4 NFE exome AF: 0.696

Gnomad4 OTH exome AF: 0.674

GnomAD4 genome AF: 0.551 AC: 83861 AN: 152108 Hom.: 28196 Cov.: 33 AF XY: 0.562 AC XY: 41778 AN XY: 74346

Gnomad4 AFR AF: 0.149

Gnomad4 AMR AF: 0.590

Gnomad4 ASJ AF: 0.763

Gnomad4 EAS AF: 0.934

Gnomad4 SAS AF: 0.853

Gnomad4 FIN AF: 0.730

Gnomad4 NFE AF: 0.697

Gnomad4 OTH AF: 0.586

Alfa AF: 0.572 Hom.: 4877

Bravo AF: 0.521

Asia WGS AF: 0.820 AC: 2851 AN: 3476

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 26, 2018	This variant is associated with the following publications: (PMID: 19415819) -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Dystonic disorder Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 22, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	0.54
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1876487; hg19: chr2-73114352; COSMIC: COSV52298477;