ENST00000537492.5:n.137-2224T>G

Variant names:

• chr2-104051280-T-G
• rs6758152
• ENST00000537492.5:n.137-2224T>G

Variant summary

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

The ENST00000537492.5(LINC01965):​n.137-2224T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0576 in 152,028 control chromosomes in the GnomAD database, including 337 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 0.058 (337 hom., cov: 31)
• Consequence: LINC01965 ENST00000537492.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.35
• Publications: 2 publications found

Genes affected

LINC01965 (HGNC:52790): (long intergenic non-protein coding RNA 1965)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0876 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01965	XR_001739621.2	n.158-2224T>G		intron_variant	Intron 1 of 2
LINC01965	XR_001739622.2	n.72-2224T>G		intron_variant	Intron 1 of 2
LINC01965	XR_007088674.1	n.72-2224T>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01965	ENST00000537492.5	n.137-2224T>G		intron_variant	Intron 1 of 3	4
LINC01965	ENST00000544869.5	n.116-2224T>G		intron_variant	Intron 1 of 2	4
LINC01965	ENST00000668937.1	n.70-2224T>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0576 AC: 8757 AN: 151910 Hom.: 337 Cov.: 31

Gnomad AFR AF: 0.0161

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.0478

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.000970

Gnomad SAS AF: 0.0475

Gnomad FIN AF: 0.0440

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0895

Gnomad OTH AF: 0.0569

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

GnomAD4 genome AF: 0.0576 AC: 8757 AN: 152028 Hom.: 337 Cov.: 31 AF XY: 0.0547 AC XY: 4067 AN XY: 74314

African (AFR) AF: 0.0161 AC: 667 AN: 41510

American (AMR) AF: 0.0478 AC: 729 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 358 AN: 3464

East Asian (EAS) AF: 0.000972 AC: 5 AN: 5144

South Asian (SAS) AF: 0.0477 AC: 229 AN: 4798

European-Finnish (FIN) AF: 0.0440 AC: 466 AN: 10584

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0895 AC: 6079 AN: 67954

Other (OTH) AF: 0.0563 AC: 119 AN: 2112

Alfa AF: 0.0720 Hom.: 563

Bravo AF: 0.0554

Asia WGS AF: 0.0210 AC: 73 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.5
DANN	Benign	0.52
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs6758152; hg19: chr2-104667738;