rs6758152

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000537492.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01965	ENST00000537492.5	TSL:4	n.137-2224T>G		intron	N/A
	LINC01965	ENST00000544869.5	TSL:4	n.116-2224T>G		intron	N/A
	LINC01965	ENST00000668937.1		n.70-2224T>G		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6758152;

hg19: chr2-104667738;