rs934197

Variant names:

• chr2-21044589-G-A
• rs934197

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 0.245 in 152,010 control chromosomes in the GnomAD database, including 5,134 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.24 (5134 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.839

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BP6: Variant 2-21044589-G-A is Benign according to our data. Variant chr2-21044589-G-A is described in ClinVar as [Benign]. Clinvar id is 3250497.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.315 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: 0.245 AC: 37203 AN: 151892 Hom.: 5130 Cov.: 31

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.328

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.197

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.318

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.245 AC: 37216 AN: 152010 Hom.: 5134 Cov.: 31 AF XY: 0.242 AC XY: 17956 AN XY: 74338

Gnomad4 AFR AF: 0.127

Gnomad4 AMR AF: 0.302

Gnomad4 ASJ AF: 0.197

Gnomad4 EAS AF: 0.121

Gnomad4 SAS AF: 0.144

Gnomad4 FIN AF: 0.274

Gnomad4 NFE AF: 0.318

Gnomad4 OTH AF: 0.221

Alfa AF: 0.271 Hom.: 584

Bravo AF: 0.244

Asia WGS AF: 0.142 AC: 494 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Familial hypercholesterolemia Benign:1

Jun 23, 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	-0.80
CADD	Benign	4.8
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs934197; hg19: chr2-21267461;