10-43318601-G-T

Variant names:

• chr10-43318601-G-T
• rs2503875
• ENST00000740938.1:n.113+6G>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000740938.1(LINC02633):​n.113+6G>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: LINC02633 ENST00000740938.1 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.97
• Publications: 28 publications found

Genes affected

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

LOC105378271 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378271	XR_945902.3	n.198+6G>T		splice_region_variant, intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02633	ENST00000740938.1	n.113+6G>T		splice_region_variant, intron_variant	Intron 1 of 2
LINC02633	ENST00000740939.1	n.113+6G>T		splice_region_variant, intron_variant	Intron 1 of 2
LINC02633	ENST00000740940.1	n.137+6G>T		splice_region_variant, intron_variant	Intron 1 of 2
LINC02633	ENST00000740943.1	n.196+828G>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.036
DANN	Benign	0.51
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs2503875; hg19: chr10-43814049;