2-21044589-G-A

Variant names:

• chr2-21044589-G-A
• rs934197
• ENST00000762415.1:n.288G>A

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The ENST00000762415.1(ENSG00000299295):​n.288G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. 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: ENSG00000299295 ENST00000762415.1 non_coding_transcript_exon
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.839
• Publications: 38 publications found

Genes affected

ENSG00000299295 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 VariationId 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000762415.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000299295	ENST00000762415.1		n.288G>A		non_coding_transcript_exon	Exon 2 of 3
	ENSG00000299295	ENST00000762416.1		n.400G>A		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000299295	ENST00000762411.1		n.73-329G>A		intron	N/A

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

African (AFR) AF: 0.127 AC: 5271 AN: 41478

American (AMR) AF: 0.302 AC: 4610 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.197 AC: 682 AN: 3468

East Asian (EAS) AF: 0.121 AC: 624 AN: 5154

South Asian (SAS) AF: 0.144 AC: 691 AN: 4804

European-Finnish (FIN) AF: 0.274 AC: 2904 AN: 10586

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.318 AC: 21622 AN: 67930

Other (OTH) AF: 0.221 AC: 465 AN: 2106

Alfa AF: 0.291 Hom.: 1577

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

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	4.8
DANN	Benign	0.61
PhyloP100		0.84

Splicing

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

Other links and lift over

dbSNP: rs934197; hg19: chr2-21267461;