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. The variant received -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
• Publications: 0 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=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.205 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

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	ENST00000652470.1		n.349+6433C>T		intron	N/A
	ENSG00000302303	ENST00000785650.1		n.74+7436G>A		intron	N/A
	LINC01208	ENST00000785771.1		n.69+6433C>T		intron	N/A

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

African (AFR) AF: 0.0836 AC: 3471 AN: 41524

American (AMR) AF: 0.132 AC: 2022 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.147 AC: 509 AN: 3472

East Asian (EAS) AF: 0.00117 AC: 6 AN: 5136

South Asian (SAS) AF: 0.104 AC: 502 AN: 4824

European-Finnish (FIN) AF: 0.160 AC: 1691 AN: 10590

Middle Eastern (MID) AF: 0.113 AC: 33 AN: 292

European-Non Finnish (NFE) AF: 0.208 AC: 14135 AN: 67992

Other (OTH) AF: 0.150 AC: 317 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.0
DANN	Benign	0.15
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs476906; hg19: chr3-176202694;