rs476906

Variant names:

• chr3-176484906-G-A
• rs476906
• ENST00000652470.1:n.349+6433C>T

Your query was ambiguous. Multiple possible variants found:

• chr3-176484906-G-A
• chr3-176484906-G-C

Variant summary

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

The ENST00000652470.1(LINC01208):​n.349+6433C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 152,140 control chromosomes in the GnomAD database, including 2,036 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 0.15 (2036 hom., cov: 32)
• Consequence: LINC01208 ENST00000652470.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.244

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=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.205 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	ENST00000652470.1	n.349+6433C>T		intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes AF: 0.150 AC: 22865 AN: 152024 Hom.: 2034 Cov.: 32

Gnomad AFR AF: 0.0835

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.00117

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.150 AC: 22878 AN: 152140 Hom.: 2036 Cov.: 32 AF XY: 0.145 AC XY: 10775 AN XY: 74354

Gnomad4 AFR AF: 0.0836

Gnomad4 AMR AF: 0.132

Gnomad4 ASJ AF: 0.147

Gnomad4 EAS AF: 0.00117

Gnomad4 SAS AF: 0.104

Gnomad4 FIN AF: 0.160

Gnomad4 NFE AF: 0.208

Gnomad4 OTH AF: 0.150

Alfa AF: 0.104 Hom.: 186

Bravo AF: 0.147

Asia WGS AF: 0.0480 AC: 165 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.0
DANN	Benign	0.15

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs476906; hg19: chr3-176202694;