rs1327316

Variant names:

• chr13-80134928-G-C
• rs1327316
• ENST00000776551.1:n.142-23782G>C

Your query was ambiguous. Multiple possible variants found:

• chr13-80134928-G-C
• chr13-80134928-G-T

Variant summary

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

The ENST00000776551.1(LINC01080):​n.142-23782G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.28 in 151,908 control chromosomes in the GnomAD database, including 6,034 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 (6034 hom., cov: 32)
• Consequence: LINC01080 ENST00000776551.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0480
• Publications: 7 publications found

Genes affected

LINC01080 (HGNC:49123): (long intergenic non-protein coding RNA 1080)

LOC105370275 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.415 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370275	XR_942116.3	n.189-13052C>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01080	ENST00000776551.1	n.142-23782G>C		intron_variant	Intron 1 of 1
LINC01080	ENST00000776552.1	n.356-23782G>C		intron_variant	Intron 1 of 1
LINC01080	ENST00000776553.1	n.56+3416G>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.280 AC: 42466 AN: 151788 Hom.: 6031 Cov.: 32

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.222

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.430

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.284

Gnomad MID AF: 0.173

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.280 AC: 42486 AN: 151908 Hom.: 6034 Cov.: 32 AF XY: 0.281 AC XY: 20825 AN XY: 74234

African (AFR) AF: 0.262 AC: 10844 AN: 41414

American (AMR) AF: 0.304 AC: 4640 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.261 AC: 906 AN: 3472

East Asian (EAS) AF: 0.430 AC: 2217 AN: 5160

South Asian (SAS) AF: 0.202 AC: 972 AN: 4808

European-Finnish (FIN) AF: 0.284 AC: 2990 AN: 10526

Middle Eastern (MID) AF: 0.175 AC: 51 AN: 292

European-Non Finnish (NFE) AF: 0.281 AC: 19102 AN: 67952

Other (OTH) AF: 0.266 AC: 562 AN: 2112

Alfa AF: 0.270 Hom.: 682

Bravo AF: 0.288

Asia WGS AF: 0.295 AC: 1027 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.8
DANN	Benign	0.51
PhyloP100		0.048

Splicing

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

Other links and lift over

dbSNP: rs1327316; hg19: chr13-80709063;