3-176516167-G-A

Variant names:

• chr3-176516167-G-A
• rs1454149
• ENST00000652470.1:n.281-24760C>T

Variant summary

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

The ENST00000652470.1(LINC01208):​n.281-24760C>T variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.18
• Publications: 3 publications found

Genes affected

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

ENSG00000302303 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000652470.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01208	ENST00000652470.1		n.281-24760C>T		intron	N/A
	ENSG00000302303	ENST00000785650.1		n.74+38697G>A		intron	N/A
	LINC01208	ENST00000785772.1		n.44+21525C>T		intron	N/A

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

African (AFR) AF: 0.876 AC: 36382 AN: 41548

American (AMR) AF: 0.818 AC: 12510 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.721 AC: 2505 AN: 3472

East Asian (EAS) AF: 0.883 AC: 4576 AN: 5180

South Asian (SAS) AF: 0.846 AC: 4083 AN: 4826

European-Finnish (FIN) AF: 0.700 AC: 7389 AN: 10560

Middle Eastern (MID) AF: 0.735 AC: 216 AN: 294

European-Non Finnish (NFE) AF: 0.749 AC: 50946 AN: 67998

Other (OTH) AF: 0.782 AC: 1652 AN: 2112

Alfa AF: 0.763 Hom.: 132084

Bravo AF: 0.804

Asia WGS AF: 0.867 AC: 3016 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	4.7
DANN	Benign	0.37
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs1454149; hg19: chr3-176233955;