10-43325042-A-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02633	XR_007062128.1	n.683+1342A>C		intron_variant	Intron 1 of 1
LINC02633	XR_945901.3	n.707+1342A>C		intron_variant	Intron 1 of 1
LOC105378271	XR_945902.3	n.294+4734A>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02633	ENST00000451438.1	n.36+1342A>C		intron_variant	Intron 1 of 2	3
LINC02633	ENST00000740933.1	n.554-2329A>C		intron_variant	Intron 1 of 1
LINC02633	ENST00000740934.1	n.221+2318A>C		intron_variant	Intron 1 of 1

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 v4.3

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;