rs1911557

chr5-170321650-T-Achr5-170321650-T-Cchr5-170321650-T-G

Variant summary

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

The ENST00000653905.1(LINC01366):n.190+10939T>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 0.691 in 152,114 control chromosomes in the GnomAD database, including 36,518 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 0.69 (36518 hom., cov: 33)
• Consequence: LINC01366 ENST00000653905.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.81

Genes affected

LINC01366 (HGNC:27416): (long intergenic non-protein coding RNA 1366)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.871 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
LINC01366	ENST00000653905.1	n.190+10939T>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.691 AC: 105067 AN: 151996 Hom.: 36480 Cov.: 33

Gnomad AFR AF: 0.688

Gnomad AMI AF: 0.768

Gnomad AMR AF: 0.756

Gnomad ASJ AF: 0.691

Gnomad EAS AF: 0.892

Gnomad SAS AF: 0.614

Gnomad FIN AF: 0.709

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.665

Gnomad OTH AF: 0.679

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

GnomAD4 genome AF: 0.691 AC: 105169 AN: 152114 Hom.: 36518 Cov.: 33 AF XY: 0.695 AC XY: 51685 AN XY: 74360

Gnomad4 AFR AF: 0.688

Gnomad4 AMR AF: 0.757

Gnomad4 ASJ AF: 0.691

Gnomad4 EAS AF: 0.892

Gnomad4 SAS AF: 0.615

Gnomad4 FIN AF: 0.709

Gnomad4 NFE AF: 0.665

Gnomad4 OTH AF: 0.682

Alfa AF: 0.679 Hom.: 4344

Bravo AF: 0.702

Asia WGS AF: 0.760 AC: 2642 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.25
Dann	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1911557; hg19: chr5-169748654;