rs2439430

Positions:

• chr15-66625506-G-T

Variant summary

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

The NR_110372.1(LINC01169):​n.60-38856G>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 0.5 in 148,360 control chromosomes in the GnomAD database, including 18,811 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 0.50 (18811 hom., cov: 27)
• Consequence: LINC01169 NR_110372.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0890

Genes affected

LINC01169 (HGNC:49541): (long intergenic non-protein coding RNA 1169)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.524 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01169	NR_110372.1	n.60-38856G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01169	ENST00000558797.1	n.60-38856G>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.500 AC: 74115 AN: 148258 Hom.: 18788 Cov.: 27

Gnomad AFR AF: 0.512

Gnomad AMI AF: 0.621

Gnomad AMR AF: 0.506

Gnomad ASJ AF: 0.454

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.542

Gnomad FIN AF: 0.584

Gnomad MID AF: 0.455

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.491

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

GnomAD4 genome AF: 0.500 AC: 74183 AN: 148360 Hom.: 18811 Cov.: 27 AF XY: 0.504 AC XY: 36370 AN XY: 72126

Gnomad4 AFR AF: 0.512

Gnomad4 AMR AF: 0.507

Gnomad4 ASJ AF: 0.454

Gnomad4 EAS AF: 0.242

Gnomad4 SAS AF: 0.542

Gnomad4 FIN AF: 0.584

Gnomad4 NFE AF: 0.497

Gnomad4 OTH AF: 0.487

Alfa AF: 0.495 Hom.: 10298

Bravo AF: 0.489

Asia WGS AF: 0.400 AC: 1391 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.60
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2439430; hg19: chr15-66917844;