10-33912923-G-A

Variant names:

• chr10-33912923-G-A
• rs2057227
• ENST00000434552.3:n.370+90G>A

Variant summary

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

The ENST00000434552.3(LINC02629):​n.370+90G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.654 in 151,678 control chromosomes in the GnomAD database, including 32,735 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 0.65 (32721 hom., cov: 30)
  • Exomes 𝑓: 0.49 (14 hom.)
• Consequence: LINC02629 ENST00000434552.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20
• Publications: 1 publications found

Genes affected

LINC02629 (HGNC:54108): (long intergenic non-protein coding RNA 2629)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.772 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000434552.3. 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
	LINC02629	NR_170279.1		n.712+90G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02629	ENST00000434552.3	TSL:5	n.370+90G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.654 AC: 99018 AN: 151452 Hom.: 32704 Cov.: 30

Gnomad AFR AF: 0.694

Gnomad AMI AF: 0.654

Gnomad AMR AF: 0.726

Gnomad ASJ AF: 0.657

Gnomad EAS AF: 0.679

Gnomad SAS AF: 0.792

Gnomad FIN AF: 0.672

Gnomad MID AF: 0.634

Gnomad NFE AF: 0.599

Gnomad OTH AF: 0.659

GnomAD4 exome AF: 0.491 AC: 53 AN: 108 Hom.: 14 AF XY: 0.530 AC XY: 35 AN XY: 66

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 2 AN: 2

East Asian (EAS) AF: 1.00 AC: 2 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.424 AC: 28 AN: 66

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.567 AC: 17 AN: 30

Other (OTH) AF: 0.500 AC: 4 AN: 8

GnomAD4 genome AF: 0.654 AC: 99083 AN: 151570 Hom.: 32721 Cov.: 30 AF XY: 0.663 AC XY: 49116 AN XY: 74080

African (AFR) AF: 0.693 AC: 28555 AN: 41188

American (AMR) AF: 0.726 AC: 11066 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.657 AC: 2279 AN: 3470

East Asian (EAS) AF: 0.679 AC: 3484 AN: 5130

South Asian (SAS) AF: 0.793 AC: 3812 AN: 4806

European-Finnish (FIN) AF: 0.672 AC: 7063 AN: 10512

Middle Eastern (MID) AF: 0.630 AC: 184 AN: 292

European-Non Finnish (NFE) AF: 0.599 AC: 40662 AN: 67922

Other (OTH) AF: 0.657 AC: 1382 AN: 2104

Alfa AF: 0.631 Hom.: 53201

Bravo AF: 0.657

Asia WGS AF: 0.714 AC: 2481 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.021
DANN	Benign	0.15
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs2057227; hg19: chr10-34201851;