rs7213314

Variant names:

• chr17-68689706-C-T
• rs7213314
• ENST00000587999.1:n.199-73784C>T

Variant summary

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

The ENST00000587999.1(LINC01482):​n.199-73784C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0937 in 152,252 control chromosomes in the GnomAD database, including 877 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 0.094 (877 hom., cov: 33)
• Consequence: LINC01482 ENST00000587999.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.576
• Publications: 9 publications found

Genes affected

LINC01482 (HGNC:51128): (long intergenic non-protein coding RNA 1482)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.166 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
LINC01482	ENST00000587999.1	n.199-73784C>T		intron_variant	Intron 2 of 2	3
LINC01482	ENST00000589610.5	n.128+30971C>T		intron_variant	Intron 2 of 3	3

Frequencies

GnomAD3 genomes AF: 0.0936 AC: 14246 AN: 152134 Hom.: 874 Cov.: 33

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.0459

Gnomad ASJ AF: 0.0862

Gnomad EAS AF: 0.00404

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.0870

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0639

Gnomad OTH AF: 0.0831

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

GnomAD4 genome AF: 0.0937 AC: 14260 AN: 152252 Hom.: 877 Cov.: 33 AF XY: 0.0942 AC XY: 7013 AN XY: 74446

African (AFR) AF: 0.169 AC: 7034 AN: 41528

American (AMR) AF: 0.0458 AC: 701 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0862 AC: 299 AN: 3470

East Asian (EAS) AF: 0.00405 AC: 21 AN: 5180

South Asian (SAS) AF: 0.148 AC: 713 AN: 4824

European-Finnish (FIN) AF: 0.0870 AC: 923 AN: 10612

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0638 AC: 4343 AN: 68022

Other (OTH) AF: 0.0841 AC: 178 AN: 2116

Alfa AF: 0.103 Hom.: 409

Bravo AF: 0.0923

Asia WGS AF: 0.0930 AC: 323 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.1
DANN	Benign	0.50
PhyloP100		0.58

Splicing

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

Other links and lift over

dbSNP: rs7213314; hg19: chr17-66685847;