5-125208637-T-C

Variant names:

• chr5-125208637-T-C
• rs6595593
• ENST00000647105.1:n.288-116715T>C

Variant summary

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

The ENST00000647105.1(LINC02240):​n.288-116715T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.884 in 151,958 control chromosomes in the GnomAD database, including 59,993 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 0.88 (59993 hom., cov: 30)
• Consequence: LINC02240 ENST00000647105.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.01
• Publications: 3 publications found

Genes affected

LINC02240 (HGNC:53118): (long intergenic non-protein coding RNA 2240)

LOC101927421 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.951 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927421	NR_109882.1	n.377+39011T>C		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02240	ENST00000647105.1	n.288-116715T>C		intron_variant	Intron 2 of 6
LINC02240	ENST00000825646.1	n.278+39011T>C		intron_variant	Intron 4 of 5
LINC02240	ENST00000825648.1	n.276+39011T>C		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.884 AC: 134231 AN: 151840 Hom.: 59950 Cov.: 30

Gnomad AFR AF: 0.798

Gnomad AMI AF: 0.987

Gnomad AMR AF: 0.805

Gnomad ASJ AF: 0.960

Gnomad EAS AF: 0.671

Gnomad SAS AF: 0.905

Gnomad FIN AF: 0.918

Gnomad MID AF: 0.940

Gnomad NFE AF: 0.958

Gnomad OTH AF: 0.899

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

GnomAD4 genome AF: 0.884 AC: 134321 AN: 151958 Hom.: 59993 Cov.: 30 AF XY: 0.879 AC XY: 65272 AN XY: 74242

African (AFR) AF: 0.798 AC: 33046 AN: 41402

American (AMR) AF: 0.804 AC: 12249 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.960 AC: 3332 AN: 3470

East Asian (EAS) AF: 0.671 AC: 3468 AN: 5168

South Asian (SAS) AF: 0.906 AC: 4357 AN: 4808

European-Finnish (FIN) AF: 0.918 AC: 9688 AN: 10558

Middle Eastern (MID) AF: 0.935 AC: 275 AN: 294

European-Non Finnish (NFE) AF: 0.958 AC: 65109 AN: 67998

Other (OTH) AF: 0.899 AC: 1899 AN: 2112

Alfa AF: 0.911 Hom.: 54920

Bravo AF: 0.871

Asia WGS AF: 0.793 AC: 2758 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.21
DANN	Benign	0.45
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs6595593; hg19: chr5-124544330;