rs13381277

Positions:

• chr18-76606653-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000670438.1(LINC00683):​n.265-62482A>G variant causes a intron, non coding transcript 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 ENST00000670438.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.06

Genes affected

LINC00683 (HGNC:44467): (long intergenic non-protein coding RNA 683)

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00683	ENST00000670438.1	n.265-62482A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.172

Gnomad4 AMR AF: 0.0848

Gnomad4 ASJ AF: 0.0865

Gnomad4 EAS AF: 0.0701

Gnomad4 SAS AF: 0.170

Gnomad4 FIN AF: 0.0434

Gnomad4 NFE AF: 0.0635

Gnomad4 OTH AF: 0.0850

Alfa AF: 0.0692 Hom.: 841

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13381277; hg19: chr18-74318610;