10-43325932-C-T

Position:

• chr10-43325932-C-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000285712 (HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LINC02633	XR_007062128.1	n.684-620C>T		intron_variant
LINC02633	XR_945901.3	n.708-1439C>T		intron_variant
LOC105378271	XR_945902.3	n.294+5624C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000285712	ENST00000650340.1	n.1491G>A		non_coding_transcript_exon_variant	3/3
LINC02633	ENST00000451438.1	n.37-1439C>T		intron_variant		3

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

Gnomad4 AFR AF: 0.551

Gnomad4 AMR AF: 0.833

Gnomad4 ASJ AF: 0.883

Gnomad4 EAS AF: 0.705

Gnomad4 SAS AF: 0.742

Gnomad4 FIN AF: 0.822

Gnomad4 NFE AF: 0.895

Gnomad4 OTH AF: 0.819

Alfa AF: 0.879 Hom.: 45819

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2460535; hg19: chr10-43821380;