rs512535

Positions:

• chr2-21044910-T-C

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 0.462 in 152,018 control chromosomes in the GnomAD database, including 17,914 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.46 (17914 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.324

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BP6: Variant 2-21044910-T-C is Benign according to our data. Variant chr2-21044910-T-C is described in ClinVar as [Benign]. Clinvar id is 3250498.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.772 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.21044910T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.463 AC: 70277 AN: 151900 Hom.: 17914 Cov.: 32

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.557

Gnomad AMR AF: 0.493

Gnomad ASJ AF: 0.446

Gnomad EAS AF: 0.793

Gnomad SAS AF: 0.698

Gnomad FIN AF: 0.578

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.531

Gnomad OTH AF: 0.499

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.462 AC: 70271 AN: 152018 Hom.: 17914 Cov.: 32 AF XY: 0.470 AC XY: 34884 AN XY: 74284

Gnomad4 AFR AF: 0.237

Gnomad4 AMR AF: 0.493

Gnomad4 ASJ AF: 0.446

Gnomad4 EAS AF: 0.792

Gnomad4 SAS AF: 0.698

Gnomad4 FIN AF: 0.578

Gnomad4 NFE AF: 0.531

Gnomad4 OTH AF: 0.501

Alfa AF: 0.449 Hom.: 1600

Bravo AF: 0.442

Asia WGS AF: 0.714 AC: 2483 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Familial hypercholesterolemia Benign:1

Benign, criteria provided, single submitter

clinical testing

GENinCode PLC

Jun 30, 2022

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.0
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs512535; hg19: chr2-21267782;