rs11121129

chr1-8208035-G-A

Variant summary

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

The ENST00000670361.1(LINC01714):n.239-632G>A 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 0.259 in 152,034 control chromosomes in the GnomAD database, including 5,403 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 0.26 (5403 hom., cov: 32)
• Consequence: LINC01714 ENST00000670361.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.639

Genes affected

LINC01714 (HGNC:52501): (long intergenic non-protein coding RNA 1714)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.365 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01714	ENST00000670361.1	n.239-632G>A		intron_variant, non_coding_transcript_variant
LINC01714	ENST00000635451.1	n.449-632G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.259 AC: 39406 AN: 151916 Hom.: 5400 Cov.: 32

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.259 AC: 39411 AN: 152034 Hom.: 5403 Cov.: 32 AF XY: 0.258 AC XY: 19169 AN XY: 74314

Gnomad4 AFR AF: 0.173

Gnomad4 AMR AF: 0.373

Gnomad4 ASJ AF: 0.220

Gnomad4 EAS AF: 0.286

Gnomad4 SAS AF: 0.292

Gnomad4 FIN AF: 0.235

Gnomad4 NFE AF: 0.288

Gnomad4 OTH AF: 0.254

Alfa AF: 0.282 Hom.: 8197

Bravo AF: 0.268

Asia WGS AF: 0.301 AC: 1048 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	5.5
Dann	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11121129; hg19: chr1-8268095;