chr3-176769680-A-T

Variant names:

• chr3-176769680-A-T
• rs9882505
• ENST00000428516.1:n.198+84029T>A

Variant summary

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

The ENST00000794389.1(LINC01208):​n.187-47695T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.15 (446 hom., cov: 0)
• Consequence: LINC01208 ENST00000794389.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0610
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.256 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000794389.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01208	ENST00000428516.1	TSL:5	n.198+84029T>A		intron	N/A
	LINC01208	ENST00000794389.1		n.187-47695T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.151 AC: 3913 AN: 25880 Hom.: 445 Cov.: 0

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.0656

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.234

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.273

Gnomad NFE AF: 0.0930

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.151 AC: 3924 AN: 25910 Hom.: 446 Cov.: 0 AF XY: 0.159 AC XY: 1898 AN XY: 11904

African (AFR) AF: 0.267 AC: 1742 AN: 6534

American (AMR) AF: 0.176 AC: 392 AN: 2224

Ashkenazi Jewish (ASJ) AF: 0.118 AC: 91 AN: 768

East Asian (EAS) AF: 0.233 AC: 197 AN: 844

South Asian (SAS) AF: 0.119 AC: 57 AN: 480

European-Finnish (FIN) AF: 0.122 AC: 109 AN: 896

Middle Eastern (MID) AF: 0.273 AC: 6 AN: 22

European-Non Finnish (NFE) AF: 0.0931 AC: 1264 AN: 13584

Other (OTH) AF: 0.159 AC: 50 AN: 314

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.7
DANN	Benign	0.32
PhyloP100		0.061

Splicing

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

Other links and lift over

dbSNP: rs9882505; hg19: chr3-176487468;