rs9282608

Positions:

• chr2-21044222-G-A

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 0.0202 in 269,094 control chromosomes in the GnomAD database, including 190 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.027 (150 hom., cov: 32)
  • Exomes 𝑓: 0.012 (40 hom.)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.187

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BP6: Variant 2-21044222-G-A is Benign according to our data. Variant chr2-21044222-G-A is described in ClinVar as [Benign]. Clinvar id is 3250494.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0749 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: 0.0264 AC: 4017 AN: 152210 Hom.: 147 Cov.: 32

Gnomad AFR AF: 0.0710

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0254

Gnomad ASJ AF: 0.0135

Gnomad EAS AF: 0.0811

Gnomad SAS AF: 0.00723

Gnomad FIN AF: 0.00395

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00148

Gnomad OTH AF: 0.0201

GnomAD4 exome AF: 0.0119 AC: 1392 AN: 116764 Hom.: 40 AF XY: 0.0111 AC XY: 676 AN XY: 60780

Gnomad4 AFR exome AF: 0.0669

Gnomad4 AMR exome AF: 0.0241

Gnomad4 ASJ exome AF: 0.0131

Gnomad4 EAS exome AF: 0.0822

Gnomad4 SAS exome AF: 0.00278

Gnomad4 FIN exome AF: 0.00218

Gnomad4 NFE exome AF: 0.00122

Gnomad4 OTH exome AF: 0.0127

GnomAD4 genome AF: 0.0266 AC: 4052 AN: 152330 Hom.: 150 Cov.: 32 AF XY: 0.0263 AC XY: 1958 AN XY: 74502

Gnomad4 AFR AF: 0.0715

Gnomad4 AMR AF: 0.0254

Gnomad4 ASJ AF: 0.0135

Gnomad4 EAS AF: 0.0813

Gnomad4 SAS AF: 0.00724

Gnomad4 FIN AF: 0.00395

Gnomad4 NFE AF: 0.00148

Gnomad4 OTH AF: 0.0218

Alfa AF: 0.0197 Hom.: 7

Bravo AF: 0.0328

Asia WGS AF: 0.0460 AC: 162 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 23, 2022

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	12
DANN	Benign	0.94

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9282608; hg19: chr2-21267094;