2-103928877-T-C

Variant names:

• chr2-103928877-T-C
• rs1348117
• ENST00000537492.5:n.136+54432T>C

Variant summary

Our verdict is Benign. The variant received -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
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.25 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

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01965	ENST00000537492.5	TSL:4	n.136+54432T>C		intron	N/A
	LINC01965	ENST00000544869.5	TSL:4	n.115+54432T>C		intron	N/A
	LINC01965	ENST00000655320.2		n.297-30417T>C		intron	N/A

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

African (AFR) AF: 0.0251 AC: 1044 AN: 41578

American (AMR) AF: 0.112 AC: 1707 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.00721 AC: 25 AN: 3466

East Asian (EAS) AF: 0.262 AC: 1351 AN: 5160

South Asian (SAS) AF: 0.0423 AC: 204 AN: 4822

European-Finnish (FIN) AF: 0.0283 AC: 300 AN: 10610

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0135 AC: 915 AN: 67998

Other (OTH) AF: 0.0374 AC: 79 AN: 2114

Alfa AF: 0.0245 Hom.: 254

Bravo AF: 0.0455

Asia WGS AF: 0.152 AC: 525 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.64
DANN	Benign	0.57
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs1348117; hg19: chr2-104545335;