rs11896968

Variant names:

• chr2-34118794-C-T
• rs11896968
• ENST00000366209.6:n.390-167849C>T

Variant summary

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

The NR_126403.1(LINC01317):​n.390-167849C>T variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.446
• Publications: 1 publications found

Genes affected

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

LINC01317 (HGNC:50523): (long intergenic non-protein coding RNA 1317)

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_126403.1. 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
	LINC01317	NR_126403.1		n.390-167849C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01320	ENST00000366209.6	TSL:5	n.390-167849C>T		intron	N/A

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

African (AFR) AF: 0.0236 AC: 979 AN: 41508

American (AMR) AF: 0.0753 AC: 1151 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.130 AC: 451 AN: 3470

East Asian (EAS) AF: 0.00154 AC: 8 AN: 5178

South Asian (SAS) AF: 0.0858 AC: 412 AN: 4802

European-Finnish (FIN) AF: 0.0705 AC: 748 AN: 10604

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.104 AC: 7100 AN: 67978

Other (OTH) AF: 0.0786 AC: 166 AN: 2112

Alfa AF: 0.0779 Hom.: 66

Bravo AF: 0.0720

Asia WGS AF: 0.0310 AC: 109 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.1
DANN	Benign	0.52
PhyloP100		-0.45
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs11896968; hg19: chr2-34343861;