rs2493654

Positions:

• chr10-43325042-A-C
• chr10-43325042-A-G

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LINC02633 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LINC02633	XR_007062128.1	n.683+1342A>C		intron_variant
LINC02633	XR_945901.3	n.707+1342A>C		intron_variant
LOC105378271	XR_945902.3	n.294+4734A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02633	ENST00000451438.1	n.36+1342A>C		intron_variant		3

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

Gnomad4 AFR AF: 0.442

Gnomad4 AMR AF: 0.421

Gnomad4 ASJ AF: 0.480

Gnomad4 EAS AF: 0.537

Gnomad4 SAS AF: 0.558

Gnomad4 FIN AF: 0.488

Gnomad4 NFE AF: 0.402

Gnomad4 OTH AF: 0.431

Alfa AF: 0.342 Hom.: 1379

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2493654; hg19: chr10-43820490;