3-176522750-A-T

Variant names:

• chr3-176522750-A-T
• rs2862479
• ENST00000652470.1:n.281-31343T>A

Variant summary

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

The ENST00000652470.1(LINC01208):​n.281-31343T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.814 in 152,080 control chromosomes in the GnomAD database, including 50,824 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 (50824 hom., cov: 32)
• Consequence: LINC01208 ENST00000652470.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.520
• Publications: 4 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=-0.92).
• 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.281-31343T>A		intron	N/A
	ENSG00000302303	ENST00000785650.1		n.75-35971A>T		intron	N/A
	LINC01208	ENST00000785772.1		n.44+14942T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.814 AC: 123739 AN: 151962 Hom.: 50760 Cov.: 32

Gnomad AFR AF: 0.888

Gnomad AMI AF: 0.732

Gnomad AMR AF: 0.836

Gnomad ASJ AF: 0.747

Gnomad EAS AF: 0.986

Gnomad SAS AF: 0.855

Gnomad FIN AF: 0.735

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.766

Gnomad OTH AF: 0.799

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

GnomAD4 genome AF: 0.814 AC: 123864 AN: 152080 Hom.: 50824 Cov.: 32 AF XY: 0.816 AC XY: 60631 AN XY: 74342

African (AFR) AF: 0.889 AC: 36887 AN: 41510

American (AMR) AF: 0.836 AC: 12778 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.747 AC: 2591 AN: 3470

East Asian (EAS) AF: 0.986 AC: 5103 AN: 5176

South Asian (SAS) AF: 0.856 AC: 4129 AN: 4822

European-Finnish (FIN) AF: 0.735 AC: 7750 AN: 10546

Middle Eastern (MID) AF: 0.745 AC: 219 AN: 294

European-Non Finnish (NFE) AF: 0.766 AC: 52051 AN: 67956

Other (OTH) AF: 0.799 AC: 1690 AN: 2114

Alfa AF: 0.801 Hom.: 6109

Bravo AF: 0.823

Asia WGS AF: 0.921 AC: 3203 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.1
DANN	Benign	0.38
PhyloP100		0.52

Splicing

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

Other links and lift over

dbSNP: rs2862479; hg19: chr3-176240538;