chr5-90225064-T-C

Variant names:

• chr5-90225064-T-C
• rs2916601
• ENST00000505712.6:n.239-24536A>G

Variant summary

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

The ENST00000505712.6(LINC01339):​n.239-24536A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.79 in 152,124 control chromosomes in the GnomAD database, including 49,273 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 0.79 (49273 hom., cov: 31)
• Consequence: LINC01339 ENST00000505712.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52
• Publications: 6 publications found

Genes affected

LINC01339 (HGNC:50549): (long intergenic non-protein coding RNA 1339)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.915 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01339	NR_120601.1	n.270-24536A>G		intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01339	ENST00000505712.6	n.239-24536A>G		intron_variant	Intron 3 of 5	2
LINC01339	ENST00000518436.5	n.179+35482A>G		intron_variant	Intron 3 of 4	3
LINC01339	ENST00000524094.3	n.256+35482A>G		intron_variant	Intron 3 of 4	3

Frequencies

GnomAD3 genomes AF: 0.791 AC: 120184 AN: 152006 Hom.: 49266 Cov.: 31

Gnomad AFR AF: 0.546

Gnomad AMI AF: 0.726

Gnomad AMR AF: 0.869

Gnomad ASJ AF: 0.888

Gnomad EAS AF: 0.937

Gnomad SAS AF: 0.838

Gnomad FIN AF: 0.894

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.886

Gnomad OTH AF: 0.818

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

GnomAD4 genome AF: 0.790 AC: 120223 AN: 152124 Hom.: 49273 Cov.: 31 AF XY: 0.792 AC XY: 58943 AN XY: 74382

African (AFR) AF: 0.545 AC: 22597 AN: 41446

American (AMR) AF: 0.869 AC: 13284 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.888 AC: 3084 AN: 3472

East Asian (EAS) AF: 0.937 AC: 4834 AN: 5160

South Asian (SAS) AF: 0.839 AC: 4046 AN: 4822

European-Finnish (FIN) AF: 0.894 AC: 9484 AN: 10612

Middle Eastern (MID) AF: 0.844 AC: 248 AN: 294

European-Non Finnish (NFE) AF: 0.886 AC: 60259 AN: 68014

Other (OTH) AF: 0.816 AC: 1725 AN: 2114

Alfa AF: 0.852 Hom.: 32190

Bravo AF: 0.778

Asia WGS AF: 0.835 AC: 2902 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.082
DANN	Benign	0.54
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs2916601; hg19: chr5-89520881;