5-170321650-T-A

Variant names:

• chr5-170321650-T-A
• rs1911557
• ENST00000653905.1:n.190+10939T>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000653905.1(LINC01366):​n.190+10939T>A variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.81
• Publications: 0 publications found

Genes affected

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

ENSG00000300272 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000653905.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01366	ENST00000653905.1		n.190+10939T>A		intron	N/A
	LINC01366	ENST00000770366.1		n.332+10939T>A		intron	N/A
	ENSG00000300272	ENST00000770538.1		n.598-3655A>T		intron	N/A

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

African (AFR) AF: 0.688 AC: 28554 AN: 41488

American (AMR) AF: 0.757 AC: 11575 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.691 AC: 2397 AN: 3470

East Asian (EAS) AF: 0.892 AC: 4622 AN: 5180

South Asian (SAS) AF: 0.615 AC: 2965 AN: 4822

European-Finnish (FIN) AF: 0.709 AC: 7497 AN: 10576

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.665 AC: 45230 AN: 67972

Other (OTH) AF: 0.682 AC: 1438 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.25
DANN	Benign	0.46
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs1911557; hg19: chr5-169748654;