3-176769680-A-T

Variant names:

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

Variant summary

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

The ENST00000428516.1(LINC01208):​n.198+84029T>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 ENST00000428516.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0610

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.256 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01208	ENST00000428516.1	n.198+84029T>A		intron_variant	Intron 2 of 4	5

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

Gnomad4 AFR AF: 0.267

Gnomad4 AMR AF: 0.176

Gnomad4 ASJ AF: 0.118

Gnomad4 EAS AF: 0.233

Gnomad4 SAS AF: 0.119

Gnomad4 FIN AF: 0.122

Gnomad4 NFE AF: 0.0931

Gnomad4 OTH AF: 0.159

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9882505; hg19: chr3-176487468;