rs11896968

chr2-34118794-C-T

Variant summary

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

The NR_126403.1(LINC01317):n.390-167849C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0733 in 152,142 control chromosomes in the GnomAD database, including 511 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 0.073 (511 hom., cov: 32)
• Consequence: LINC01317 NR_126403.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.446

Genes affected

LINC01320 (HGNC:50526): (long intergenic non-protein coding RNA 1320)

LINC01317 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.102 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01317	NR_126403.1	n.390-167849C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01320	ENST00000366209.6	n.390-167849C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0734 AC: 11162 AN: 152024 Hom.: 511 Cov.: 32

Gnomad AFR AF: 0.0236

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.0755

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0855

Gnomad FIN AF: 0.0705

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.0794

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

GnomAD4 genome AF: 0.0733 AC: 11158 AN: 152142 Hom.: 511 Cov.: 32 AF XY: 0.0722 AC XY: 5368 AN XY: 74400

Gnomad4 AFR AF: 0.0236

Gnomad4 AMR AF: 0.0753

Gnomad4 ASJ AF: 0.130

Gnomad4 EAS AF: 0.00154

Gnomad4 SAS AF: 0.0858

Gnomad4 FIN AF: 0.0705

Gnomad4 NFE AF: 0.104

Gnomad4 OTH AF: 0.0786

Alfa AF: 0.0803 Hom.: 66

Bravo AF: 0.0720

Asia WGS AF: 0.0310 AC: 109 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	2.1
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11896968; hg19: chr2-34343861;