chr13-80031651-A-C

Variant names:

• chr13-80031651-A-C
• rs7995973
• ENST00000648514.1:n.827+15383T>G

Variant summary

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

The ENST00000648514.1(ENSG00000284196):​n.827+15383T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.334 in 151,962 control chromosomes in the GnomAD database, including 8,707 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 0.33 (8707 hom., cov: 32)
• Consequence: ENSG00000284196 ENST00000648514.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.49
• Publications: 5 publications found

Genes affected

ENSG00000284196 (HGNC:):

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.49).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000648514.1. 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
	ENSG00000284196	ENST00000648514.1		n.827+15383T>G		intron	N/A
	LINC01080	ENST00000776551.1		n.141+20398A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.334 AC: 50777 AN: 151844 Hom.: 8699 Cov.: 32

Gnomad AFR AF: 0.380

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.251

Gnomad SAS AF: 0.371

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.334 AC: 50821 AN: 151962 Hom.: 8707 Cov.: 32 AF XY: 0.333 AC XY: 24692 AN XY: 74244

African (AFR) AF: 0.380 AC: 15766 AN: 41452

American (AMR) AF: 0.268 AC: 4097 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.379 AC: 1314 AN: 3468

East Asian (EAS) AF: 0.250 AC: 1291 AN: 5158

South Asian (SAS) AF: 0.370 AC: 1784 AN: 4820

European-Finnish (FIN) AF: 0.297 AC: 3135 AN: 10546

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.329 AC: 22376 AN: 67942

Other (OTH) AF: 0.353 AC: 745 AN: 2110

Alfa AF: 0.337 Hom.: 7502

Bravo AF: 0.332

Asia WGS AF: 0.347 AC: 1210 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	13
DANN	Benign	0.62
PhyloP100		2.5

Splicing

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

Other links and lift over

dbSNP: rs7995973; hg19: chr13-80605786;