2-21044910-T-C

Variant names:

• chr2-21044910-T-C
• rs512535

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: Unknown
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.324

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

Jun 30, 2022

GENinCode PLC

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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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;