rs476906

Positions:

• 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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01208	ENST00000652470.1	n.349+6433C>T		intron_variant, non_coding_transcript_variant

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;