rs301193

Variant names:

• chr3-176421737-T-C
• rs301193
• ENST00000652470.1:n.350-741A>G

Variant summary

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

The ENST00000652470.1(LINC01208):​n.350-741A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 152,182 control chromosomes in the GnomAD database, including 1,203 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 0.12 (1203 hom., cov: 32)
• Consequence: LINC01208 ENST00000652470.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.222

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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.157 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.350-741A>G		intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17589 AN: 152064 Hom.: 1200 Cov.: 32

Gnomad AFR AF: 0.0699

Gnomad AMI AF: 0.0768

Gnomad AMR AF: 0.0984

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.000961

Gnomad SAS AF: 0.0577

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.0577

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.116 AC: 17603 AN: 152182 Hom.: 1203 Cov.: 32 AF XY: 0.110 AC XY: 8217 AN XY: 74386

Gnomad4 AFR AF: 0.0698

Gnomad4 AMR AF: 0.0983

Gnomad4 ASJ AF: 0.114

Gnomad4 EAS AF: 0.000963

Gnomad4 SAS AF: 0.0578

Gnomad4 FIN AF: 0.128

Gnomad4 NFE AF: 0.159

Gnomad4 OTH AF: 0.126

Alfa AF: 0.144 Hom.: 758

Bravo AF: 0.114

Asia WGS AF: 0.0370 AC: 129 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs301193; hg19: chr3-176139525;