10-43325932-C-T

Variant names:

• chr10-43325932-C-T
• rs2460535
• ENST00000650340.1:n.1491G>A

Variant summary

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

The ENST00000650340.1(ENSG00000285712):​n.1491G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.777 in 152,194 control chromosomes in the GnomAD database, including 47,667 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 0.78 (47667 hom., cov: 33)
• Consequence: ENSG00000285712 ENST00000650340.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20
• Publications: 7 publications found

Genes affected

ENSG00000285712 (HGNC:):

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.889 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02633	XR_007062128.1	n.684-620C>T		intron_variant	Intron 1 of 1
LINC02633	XR_945901.3	n.708-1439C>T		intron_variant	Intron 1 of 1
LOC105378271	XR_945902.3	n.294+5624C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285712	ENST00000650340.1	n.1491G>A		non_coding_transcript_exon_variant	Exon 3 of 3
LINC02633	ENST00000451438.1	n.37-1439C>T		intron_variant	Intron 1 of 2	3
LINC02633	ENST00000740933.1	n.554-1439C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.778 AC: 118284 AN: 152076 Hom.: 47664 Cov.: 33

Gnomad AFR AF: 0.552

Gnomad AMI AF: 0.930

Gnomad AMR AF: 0.833

Gnomad ASJ AF: 0.883

Gnomad EAS AF: 0.706

Gnomad SAS AF: 0.741

Gnomad FIN AF: 0.822

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.895

Gnomad OTH AF: 0.820

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

GnomAD4 genome AF: 0.777 AC: 118319 AN: 152194 Hom.: 47667 Cov.: 33 AF XY: 0.772 AC XY: 57466 AN XY: 74402

African (AFR) AF: 0.551 AC: 22853 AN: 41482

American (AMR) AF: 0.833 AC: 12739 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.883 AC: 3065 AN: 3470

East Asian (EAS) AF: 0.705 AC: 3646 AN: 5168

South Asian (SAS) AF: 0.742 AC: 3573 AN: 4818

European-Finnish (FIN) AF: 0.822 AC: 8723 AN: 10610

Middle Eastern (MID) AF: 0.861 AC: 253 AN: 294

European-Non Finnish (NFE) AF: 0.895 AC: 60888 AN: 68028

Other (OTH) AF: 0.819 AC: 1731 AN: 2114

Alfa AF: 0.864 Hom.: 57089

Bravo AF: 0.769

Asia WGS AF: 0.695 AC: 2420 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	1.4
DANN	Benign	0.64
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs2460535; hg19: chr10-43821380;