13-80065389-T-C

Variant names:

• chr13-80065389-T-C
• rs7990916
• ENST00000639897.1:n.224+4390A>G

Variant summary

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

The ENST00000639897.1(ENSG00000284196):​n.224+4390A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.658 in 152,072 control chromosomes in the GnomAD database, including 33,514 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 0.66 (33514 hom., cov: 32)
• Consequence: ENSG00000284196 ENST00000639897.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308
• Publications: 11 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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.871 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
ENSG00000284196	ENST00000639897.1	n.224+4390A>G		intron_variant	Intron 3 of 8	5
ENSG00000284196	ENST00000639964.1	n.357+4390A>G		intron_variant	Intron 4 of 5	4
ENSG00000284196	ENST00000639965.1	n.214+8000A>G		intron_variant	Intron 2 of 5	5

Frequencies

GnomAD3 genomes AF: 0.658 AC: 99934 AN: 151956 Hom.: 33485 Cov.: 32

Gnomad AFR AF: 0.537

Gnomad AMI AF: 0.598

Gnomad AMR AF: 0.761

Gnomad ASJ AF: 0.784

Gnomad EAS AF: 0.893

Gnomad SAS AF: 0.830

Gnomad FIN AF: 0.597

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.680

Gnomad OTH AF: 0.688

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

GnomAD4 genome AF: 0.658 AC: 100007 AN: 152072 Hom.: 33514 Cov.: 32 AF XY: 0.660 AC XY: 49060 AN XY: 74338

African (AFR) AF: 0.537 AC: 22254 AN: 41462

American (AMR) AF: 0.761 AC: 11636 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.784 AC: 2721 AN: 3470

East Asian (EAS) AF: 0.893 AC: 4622 AN: 5178

South Asian (SAS) AF: 0.830 AC: 3993 AN: 4812

European-Finnish (FIN) AF: 0.597 AC: 6319 AN: 10576

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.680 AC: 46251 AN: 67980

Other (OTH) AF: 0.692 AC: 1457 AN: 2106

Alfa AF: 0.683 Hom.: 20543

Bravo AF: 0.664

Asia WGS AF: 0.832 AC: 2893 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.8
DANN	Benign	0.72
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs7990916; hg19: chr13-80639524;