10-68241124-C-T

Variant names:

• chr10-68241124-C-T
• rs1900004
• ENST00000444086.1:n.60+1196G>A

Variant summary

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

The ENST00000444086.1(LINC02640):​n.60+1196G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.384 in 151,974 control chromosomes in the GnomAD database, including 13,903 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 0.38 (13903 hom., cov: 31)
• Consequence: LINC02640 ENST00000444086.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75
• Publications: 52 publications found

Genes affected

LINC02640 (HGNC:54123): (long intergenic non-protein coding RNA 2640)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.665 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02640	XR_001747481.1	n.103+1196G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02640	ENST00000444086.1	n.60+1196G>A		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.384 AC: 58305 AN: 151856 Hom.: 13868 Cov.: 31

Gnomad AFR AF: 0.672

Gnomad AMI AF: 0.412

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.346

Gnomad SAS AF: 0.295

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.332

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

GnomAD4 genome AF: 0.384 AC: 58403 AN: 151974 Hom.: 13903 Cov.: 31 AF XY: 0.387 AC XY: 28722 AN XY: 74262

African (AFR) AF: 0.672 AC: 27837 AN: 41434

American (AMR) AF: 0.350 AC: 5339 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.317 AC: 1101 AN: 3470

East Asian (EAS) AF: 0.346 AC: 1779 AN: 5144

South Asian (SAS) AF: 0.295 AC: 1422 AN: 4816

European-Finnish (FIN) AF: 0.311 AC: 3292 AN: 10576

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.243 AC: 16482 AN: 67956

Other (OTH) AF: 0.329 AC: 696 AN: 2114

Alfa AF: 0.284 Hom.: 20397

Bravo AF: 0.405

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.8
DANN	Benign	0.45
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs1900004; hg19: chr10-70000881;