rs6078866

Variant names:

• chr20-12993919-A-G
• rs6078866
• ENST00000669657.1:n.875-14139A>G

Variant summary

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

The ENST00000669657.1(LINC01723):​n.875-14139A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.361 in 151,994 control chromosomes in the GnomAD database, including 10,150 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 0.36 (10150 hom., cov: 32)
• Consequence: LINC01723 ENST00000669657.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0110
• Publications: 3 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.428 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
LINC01723	ENST00000669657.1	n.875-14139A>G		intron_variant	Intron 4 of 4
LINC01723	ENST00000670547.1	n.877-991A>G		intron_variant	Intron 4 of 5
LINC01723	ENST00000671262.1	n.871-14139A>G		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.361 AC: 54830 AN: 151876 Hom.: 10137 Cov.: 32

Gnomad AFR AF: 0.434

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.344

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.396

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.421

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.361 AC: 54850 AN: 151994 Hom.: 10150 Cov.: 32 AF XY: 0.367 AC XY: 27229 AN XY: 74294

African (AFR) AF: 0.433 AC: 17948 AN: 41440

American (AMR) AF: 0.344 AC: 5253 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.309 AC: 1073 AN: 3470

East Asian (EAS) AF: 0.396 AC: 2041 AN: 5160

South Asian (SAS) AF: 0.421 AC: 2031 AN: 4820

European-Finnish (FIN) AF: 0.421 AC: 4448 AN: 10570

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.310 AC: 21065 AN: 67968

Other (OTH) AF: 0.328 AC: 691 AN: 2108

Alfa AF: 0.347 Hom.: 1566

Bravo AF: 0.354

Asia WGS AF: 0.404 AC: 1407 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.9
DANN	Benign	0.74
PhyloP100		0.011

Splicing

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

Other links and lift over

dbSNP: rs6078866; hg19: chr20-12974567;