3-176527254-G-T

Variant names:

• chr3-176527254-G-T
• rs1377828
• ENST00000652470.1:n.281-35847C>A

Variant summary

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

The ENST00000652470.1(LINC01208):​n.281-35847C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.809 in 152,124 control chromosomes in the GnomAD database, including 50,065 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 0.81 (50065 hom., cov: 33)
• Consequence: LINC01208 ENST00000652470.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.37
• Publications: 2 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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.963 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01208	ENST00000652470.1		n.281-35847C>A		intron	N/A
	ENSG00000302303	ENST00000785650.1		n.75-31467G>T		intron	N/A
	LINC01208	ENST00000785772.1		n.44+10438C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.808 AC: 122881 AN: 152006 Hom.: 50003 Cov.: 33

Gnomad AFR AF: 0.868

Gnomad AMI AF: 0.732

Gnomad AMR AF: 0.834

Gnomad ASJ AF: 0.746

Gnomad EAS AF: 0.986

Gnomad SAS AF: 0.855

Gnomad FIN AF: 0.735

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.766

Gnomad OTH AF: 0.793

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

GnomAD4 genome AF: 0.809 AC: 123003 AN: 152124 Hom.: 50065 Cov.: 33 AF XY: 0.810 AC XY: 60205 AN XY: 74372

African (AFR) AF: 0.869 AC: 36057 AN: 41512

American (AMR) AF: 0.835 AC: 12753 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.746 AC: 2590 AN: 3472

East Asian (EAS) AF: 0.986 AC: 5121 AN: 5194

South Asian (SAS) AF: 0.856 AC: 4126 AN: 4818

European-Finnish (FIN) AF: 0.735 AC: 7767 AN: 10572

Middle Eastern (MID) AF: 0.741 AC: 218 AN: 294

European-Non Finnish (NFE) AF: 0.766 AC: 52031 AN: 67962

Other (OTH) AF: 0.794 AC: 1672 AN: 2106

Alfa AF: 0.785 Hom.: 34711

Bravo AF: 0.815

Asia WGS AF: 0.919 AC: 3182 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	9.2
DANN	Benign	0.42
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs1377828; hg19: chr3-176245042;