rs6078860

chr20-12986090-C-T

Variant summary

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

The ENST00000669657.1(LINC01723):n.874+18880C>T 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 0.0629 in 152,172 control chromosomes in the GnomAD database, including 441 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 0.063 (441 hom., cov: 32)
• Consequence: LINC01723 ENST00000669657.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.283

Genes affected

LINC01723 (HGNC:52511): (long intergenic non-protein coding RNA 1723)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.094 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01723	ENST00000669657.1	n.874+18880C>T		intron_variant, non_coding_transcript_variant
LINC01723	ENST00000670547.1	n.877-8820C>T		intron_variant, non_coding_transcript_variant
LINC01723	ENST00000671262.1	n.870+18880C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0629 AC: 9569 AN: 152054 Hom.: 441 Cov.: 32

Gnomad AFR AF: 0.0154

Gnomad AMI AF: 0.0626

Gnomad AMR AF: 0.0535

Gnomad ASJ AF: 0.0652

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0245

Gnomad FIN AF: 0.0975

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0959

Gnomad OTH AF: 0.0717

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

GnomAD4 genome AF: 0.0629 AC: 9569 AN: 152172 Hom.: 441 Cov.: 32 AF XY: 0.0613 AC XY: 4561 AN XY: 74400

Gnomad4 AFR AF: 0.0153

Gnomad4 AMR AF: 0.0534

Gnomad4 ASJ AF: 0.0652

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0247

Gnomad4 FIN AF: 0.0975

Gnomad4 NFE AF: 0.0959

Gnomad4 OTH AF: 0.0705

Alfa AF: 0.0888 Hom.: 154

Bravo AF: 0.0565

Asia WGS AF: 0.00924 AC: 32 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	6.9
Dann	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6078860; hg19: chr20-12966738;