10-123417308-A-T

Variant names:

• chr10-123417308-A-T
• rs10510130
• ENST00000448347.5:n.587-32045A>T

Variant summary

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

The ENST00000448347.5(LINC02641):​n.587-32045A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0916 in 152,292 control chromosomes in the GnomAD database, including 885 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 0.092 (885 hom., cov: 32)
• Consequence: LINC02641 ENST00000448347.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.626
• Publications: 1 publications found

Genes affected

LINC02641 (HGNC:54125): (long intergenic non-protein coding RNA 2641)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.133 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02641	XR_002957104.1	n.6363-32045A>T		intron_variant	Intron 4 of 9
LINC02641	XR_002957105.1	n.5694-32045A>T		intron_variant	Intron 3 of 8
LINC02641	XR_007062326.1	n.8910-32045A>T		intron_variant	Intron 6 of 11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02641	ENST00000448347.5	n.587-32045A>T		intron_variant	Intron 3 of 4	3
LINC02641	ENST00000448671.2	n.539-32045A>T		intron_variant	Intron 3 of 4	3
LINC02641	ENST00000662754.1	n.337+55758A>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.0917 AC: 13956 AN: 152174 Hom.: 886 Cov.: 32

Gnomad AFR AF: 0.0254

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.0764

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.0650

Gnomad SAS AF: 0.0236

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.0996

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

GnomAD4 genome AF: 0.0916 AC: 13949 AN: 152292 Hom.: 885 Cov.: 32 AF XY: 0.0893 AC XY: 6654 AN XY: 74474

African (AFR) AF: 0.0253 AC: 1052 AN: 41566

American (AMR) AF: 0.0762 AC: 1166 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.160 AC: 556 AN: 3472

East Asian (EAS) AF: 0.0650 AC: 337 AN: 5188

South Asian (SAS) AF: 0.0240 AC: 116 AN: 4826

European-Finnish (FIN) AF: 0.112 AC: 1185 AN: 10608

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.136 AC: 9226 AN: 68020

Other (OTH) AF: 0.0981 AC: 207 AN: 2110

Alfa AF: 0.108 Hom.: 137

Bravo AF: 0.0864

Asia WGS AF: 0.0440 AC: 152 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	9.8
DANN	Benign	0.81
PhyloP100		0.63

Splicing

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

Other links and lift over

dbSNP: rs10510130; hg19: chr10-125176824;