rs13381277

Variant names:

• chr18-76606653-A-G
• rs13381277
• ENST00000583578.6:n.326-4192A>G

Variant summary

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

The ENST00000583578.6(LINC00683):​n.326-4192A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0979 in 151,670 control chromosomes in the GnomAD database, including 947 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 0.098 (947 hom., cov: 32)
• Consequence: LINC00683 ENST00000583578.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.06
• Publications: 4 publications found

Genes affected

LINC00683 (HGNC:27599): (long intergenic non-protein coding RNA 908)

LINC01927 (HGNC:52749): (long intergenic non-protein coding RNA 1927)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.169 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
LINC00683	ENST00000583578.6	n.326-4192A>G		intron_variant	Intron 2 of 3	3
LINC00683	ENST00000651044.1	n.176-4192A>G		intron_variant	Intron 2 of 5
LINC00683	ENST00000653843.1	n.509-4192A>G		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.0979 AC: 14838 AN: 151552 Hom.: 945 Cov.: 32

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.0241

Gnomad AMR AF: 0.0852

Gnomad ASJ AF: 0.0865

Gnomad EAS AF: 0.0700

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.0434

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0635

Gnomad OTH AF: 0.0821

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

GnomAD4 genome AF: 0.0979 AC: 14850 AN: 151670 Hom.: 947 Cov.: 32 AF XY: 0.0968 AC XY: 7176 AN XY: 74106

African (AFR) AF: 0.172 AC: 7088 AN: 41234

American (AMR) AF: 0.0848 AC: 1293 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.0865 AC: 300 AN: 3470

East Asian (EAS) AF: 0.0701 AC: 362 AN: 5164

South Asian (SAS) AF: 0.170 AC: 815 AN: 4794

European-Finnish (FIN) AF: 0.0434 AC: 457 AN: 10524

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0635 AC: 4316 AN: 67924

Other (OTH) AF: 0.0850 AC: 179 AN: 2106

Alfa AF: 0.0754 Hom.: 1757

Bravo AF: 0.102

Asia WGS AF: 0.151 AC: 525 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	0.14
DANN	Benign	0.42
PhyloP100		-3.1

Splicing

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

Other links and lift over

dbSNP: rs13381277; hg19: chr18-74318610;