rs1454149

Positions:

• chr3-176516167-G-A

Variant summary

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

The ENST00000652470.1(LINC01208):​n.281-24760C>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 0.795 in 152,190 control chromosomes in the GnomAD database, including 48,388 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 0.79 (48388 hom., cov: 33)
• Consequence: LINC01208 ENST00000652470.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.18

Genes affected

LINC01208 (HGNC:49639): (long intergenic non-protein coding RNA 1208)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.868 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
LINC01208	ENST00000652470.1	n.281-24760C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.794 AC: 120806 AN: 152072 Hom.: 48329 Cov.: 33

Gnomad AFR AF: 0.876

Gnomad AMI AF: 0.735

Gnomad AMR AF: 0.818

Gnomad ASJ AF: 0.721

Gnomad EAS AF: 0.884

Gnomad SAS AF: 0.845

Gnomad FIN AF: 0.700

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.749

Gnomad OTH AF: 0.782

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

GnomAD4 genome AF: 0.795 AC: 120926 AN: 152190 Hom.: 48388 Cov.: 33 AF XY: 0.795 AC XY: 59125 AN XY: 74410

Gnomad4 AFR AF: 0.876

Gnomad4 AMR AF: 0.818

Gnomad4 ASJ AF: 0.721

Gnomad4 EAS AF: 0.883

Gnomad4 SAS AF: 0.846

Gnomad4 FIN AF: 0.700

Gnomad4 NFE AF: 0.749

Gnomad4 OTH AF: 0.782

Alfa AF: 0.754 Hom.: 77063

Bravo AF: 0.804

Asia WGS AF: 0.867 AC: 3016 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	4.7
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1454149; hg19: chr3-176233955;