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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000650340.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285712	ENST00000650340.1		n.1491G>A		non_coding_transcript_exon	Exon 3 of 3
	LINC02633	ENST00000451438.1	TSL:3	n.37-1439C>T		intron	N/A
	LINC02633	ENST00000740933.1		n.554-1439C>T		intron	N/A

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 v4.9

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;