rs2282290

Variant names:

• chr1-111320829-A-G
• rs2282290
• ENST00000426321.2:n.392-2902T>C

Your query was ambiguous. Multiple possible variants found:

• chr1-111320829-A-G
• chr1-111320829-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000426321.2(ENSG00000229283):​n.392-2902T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.377 in 152,088 control chromosomes in the GnomAD database, including 11,375 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.38 (11375 hom., cov: 32)
• Consequence: ENSG00000229283 ENST00000426321.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 8 publications found

Genes affected

ENSG00000229283 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.449 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
ENSG00000229283	ENST00000426321.2	n.392-2902T>C		intron_variant	Intron 3 of 3	3
ENSG00000229283	ENST00000725074.1	n.370-2902T>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.377 AC: 57303 AN: 151970 Hom.: 11379 Cov.: 32

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.601

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.522

Gnomad EAS AF: 0.343

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.428

Gnomad OTH AF: 0.369

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

GnomAD4 genome AF: 0.377 AC: 57309 AN: 152088 Hom.: 11375 Cov.: 32 AF XY: 0.374 AC XY: 27807 AN XY: 74356

African (AFR) AF: 0.297 AC: 12306 AN: 41502

American (AMR) AF: 0.292 AC: 4459 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.522 AC: 1811 AN: 3470

East Asian (EAS) AF: 0.343 AC: 1773 AN: 5174

South Asian (SAS) AF: 0.466 AC: 2243 AN: 4818

European-Finnish (FIN) AF: 0.396 AC: 4192 AN: 10586

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.428 AC: 29056 AN: 67938

Other (OTH) AF: 0.368 AC: 777 AN: 2112

Alfa AF: 0.411 Hom.: 9245

Bravo AF: 0.363

Asia WGS AF: 0.367 AC: 1275 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.20
DANN	Benign	0.43
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs2282290; hg19: chr1-111863451;