ENST00000451438.1:n.36+1342A>C

Variant names:

• chr10-43325042-A-C
• rs2493654
• ENST00000451438.1:n.36+1342A>C

Variant summary

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

The ENST00000451438.1(LINC02633):​n.36+1342A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.433 in 152,090 control chromosomes in the GnomAD database, including 14,463 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 0.43 (14463 hom., cov: 32)
• Consequence: LINC02633 ENST00000451438.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.58
• Publications: 4 publications found

Genes affected

LINC02633 (HGNC:54116): (long intergenic non-protein coding RNA 2633)

LOC105378271 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.54 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000451438.1. 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
	LINC02633	ENST00000451438.1	TSL:3	n.36+1342A>C		intron	N/A
	LINC02633	ENST00000740933.1		n.554-2329A>C		intron	N/A
	LINC02633	ENST00000740934.1		n.221+2318A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.432 AC: 65724 AN: 151972 Hom.: 14442 Cov.: 32

Gnomad AFR AF: 0.442

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.537

Gnomad SAS AF: 0.558

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.402

Gnomad OTH AF: 0.431

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

GnomAD4 genome AF: 0.433 AC: 65786 AN: 152090 Hom.: 14463 Cov.: 32 AF XY: 0.439 AC XY: 32677 AN XY: 74352

African (AFR) AF: 0.442 AC: 18353 AN: 41480

American (AMR) AF: 0.421 AC: 6445 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.480 AC: 1666 AN: 3472

East Asian (EAS) AF: 0.537 AC: 2769 AN: 5156

South Asian (SAS) AF: 0.558 AC: 2690 AN: 4824

European-Finnish (FIN) AF: 0.488 AC: 5159 AN: 10574

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.402 AC: 27328 AN: 67970

Other (OTH) AF: 0.431 AC: 911 AN: 2116

Alfa AF: 0.347 Hom.: 1460

Bravo AF: 0.423

Asia WGS AF: 0.550 AC: 1906 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	6.6
DANN	Benign	0.79
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs2493654; hg19: chr10-43820490;