rs718617

Variant names:

• chr13-27393704-G-A
• rs718617
• ENST00000833686.1:n.90-10562G>A

Variant summary

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

The ENST00000833686.1(LINC01079):​n.90-10562G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.277 in 152,076 control chromosomes in the GnomAD database, including 6,144 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 0.28 (6144 hom., cov: 33)
• Consequence: LINC01079 ENST00000833686.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.84
• Publications: 11 publications found

Genes affected

LINC01079 (HGNC:49122): (long intergenic non-protein coding RNA 1079)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.339 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
LINC01079	ENST00000833686.1	n.90-10562G>A		intron_variant	Intron 1 of 2
LINC01079	ENST00000833687.1	n.364-2587G>A		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.277 AC: 42154 AN: 151958 Hom.: 6131 Cov.: 33

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.155

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.281

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

GnomAD4 genome AF: 0.277 AC: 42197 AN: 152076 Hom.: 6144 Cov.: 33 AF XY: 0.276 AC XY: 20501 AN XY: 74316

African (AFR) AF: 0.344 AC: 14245 AN: 41448

American (AMR) AF: 0.214 AC: 3276 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.343 AC: 1190 AN: 3466

East Asian (EAS) AF: 0.155 AC: 805 AN: 5178

South Asian (SAS) AF: 0.316 AC: 1520 AN: 4808

European-Finnish (FIN) AF: 0.306 AC: 3234 AN: 10566

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.250 AC: 17018 AN: 68000

Other (OTH) AF: 0.283 AC: 598 AN: 2114

Alfa AF: 0.254 Hom.: 21690

Bravo AF: 0.267

Asia WGS AF: 0.243 AC: 845 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	0.34
DANN	Benign	0.85
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs718617; hg19: chr13-27967841;