rs1348117

Positions:

• chr2-103928877-T-C
• chr2-103928877-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000537492.5(LINC01965):​n.136+54432T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.037 in 152,228 control chromosomes in the GnomAD database, including 341 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 0.037 (341 hom., cov: 32)
• Consequence: LINC01965 ENST00000537492.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.478

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.25 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01965	XR_001739621.2	n.157+54432T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01965	ENST00000537492.5	n.136+54432T>C		intron_variant		4
LINC01965	ENST00000544869.5	n.115+54432T>C		intron_variant		4
LINC01965	ENST00000655320.1	n.116-30417T>C		intron_variant
LINC01965	ENST00000688553.1	n.210+54432T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0369 AC: 5612 AN: 152110 Hom.: 336 Cov.: 32

Gnomad AFR AF: 0.0249

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.00721

Gnomad EAS AF: 0.262

Gnomad SAS AF: 0.0421

Gnomad FIN AF: 0.0283

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0135

Gnomad OTH AF: 0.0382

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

GnomAD4 genome AF: 0.0370 AC: 5628 AN: 152228 Hom.: 341 Cov.: 32 AF XY: 0.0393 AC XY: 2924 AN XY: 74410

Gnomad4 AFR AF: 0.0251

Gnomad4 AMR AF: 0.112

Gnomad4 ASJ AF: 0.00721

Gnomad4 EAS AF: 0.262

Gnomad4 SAS AF: 0.0423

Gnomad4 FIN AF: 0.0283

Gnomad4 NFE AF: 0.0135

Gnomad4 OTH AF: 0.0374

Alfa AF: 0.0217 Hom.: 171

Bravo AF: 0.0455

Asia WGS AF: 0.152 AC: 525 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.64
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1348117; hg19: chr2-104545335;