rs2282290

Positions:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000426321.1(ENSG00000229283):​n.149-2902T>C variant causes a intron, non coding transcript 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: ENST00000426321.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000426321.1	n.149-2902T>C		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.297

Gnomad4 AMR AF: 0.292

Gnomad4 ASJ AF: 0.522

Gnomad4 EAS AF: 0.343

Gnomad4 SAS AF: 0.466

Gnomad4 FIN AF: 0.396

Gnomad4 NFE AF: 0.428

Gnomad4 OTH AF: 0.368

Alfa AF: 0.414 Hom.: 6842

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2282290; hg19: chr1-111863451;