rs1490075

chr3-176704864-C-T

Variant summary

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

The ENST00000428516.1(LINC01208):n.199-48133G>A 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 0.12 in 152,186 control chromosomes in the GnomAD database, including 1,262 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 (1262 hom., cov: 33)
• Consequence: LINC01208 ENST00000428516.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.964

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=-0.75).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.173 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01208	ENST00000428516.1	n.199-48133G>A		intron_variant, non_coding_transcript_variant		5
LINC01208	ENST00000657476.1	n.154+15613G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18246 AN: 152068 Hom.: 1262 Cov.: 33

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.0922

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.0939

Gnomad MID AF: 0.118

Gnomad NFE AF: 0.0905

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.120 AC: 18267 AN: 152186 Hom.: 1262 Cov.: 33 AF XY: 0.121 AC XY: 9020 AN XY: 74394

Gnomad4 AFR AF: 0.177

Gnomad4 AMR AF: 0.105

Gnomad4 ASJ AF: 0.0922

Gnomad4 EAS AF: 0.137

Gnomad4 SAS AF: 0.157

Gnomad4 FIN AF: 0.0939

Gnomad4 NFE AF: 0.0905

Gnomad4 OTH AF: 0.126

Alfa AF: 0.108 Hom.: 123

Bravo AF: 0.121

Asia WGS AF: 0.167 AC: 578 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
Cadd	Benign	0.93
Dann	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1490075; hg19: chr3-176422652;