rs1448539

Positions:

• chr2-176547071-T-C

Variant summary

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

The ENST00000652995.1(LINC01117):​n.398+49276T>C 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 0.797 in 152,176 control chromosomes in the GnomAD database, including 49,526 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 0.80 (49526 hom., cov: 32)
• Consequence: LINC01117 ENST00000652995.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.348

Genes affected

LINC01117 (HGNC:49260): (long intergenic non-protein coding RNA 1117)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.914 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01117	ENST00000652995.1	n.398+49276T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.798 AC: 121279 AN: 152058 Hom.: 49507 Cov.: 32

Gnomad AFR AF: 0.605

Gnomad AMI AF: 0.942

Gnomad AMR AF: 0.856

Gnomad ASJ AF: 0.790

Gnomad EAS AF: 0.935

Gnomad SAS AF: 0.934

Gnomad FIN AF: 0.892

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.865

Gnomad OTH AF: 0.798

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

GnomAD4 genome AF: 0.797 AC: 121341 AN: 152176 Hom.: 49526 Cov.: 32 AF XY: 0.803 AC XY: 59742 AN XY: 74404

Gnomad4 AFR AF: 0.605

Gnomad4 AMR AF: 0.856

Gnomad4 ASJ AF: 0.790

Gnomad4 EAS AF: 0.936

Gnomad4 SAS AF: 0.934

Gnomad4 FIN AF: 0.892

Gnomad4 NFE AF: 0.865

Gnomad4 OTH AF: 0.798

Alfa AF: 0.852 Hom.: 25126

Bravo AF: 0.784

Asia WGS AF: 0.872 AC: 3033 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.7
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1448539; hg19: chr2-177411799;