rs6443468

Variant names:

• chr3-177565231-C-T
• rs6443468
• ENST00000439009.1:n.147+123121C>T

Variant summary

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

The ENST00000439009.1(LINC00578):​n.147+123121C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.329 in 151,792 control chromosomes in the GnomAD database, including 8,540 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 0.33 (8540 hom., cov: 30)
• Consequence: LINC00578 ENST00000439009.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.09
• Publications: 2 publications found

Genes affected

LINC00578 (HGNC:43807): (long intergenic non-protein coding RNA 578)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.49 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00578	NR_047568.1	n.289+25738C>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00578	ENST00000439009.1	n.147+123121C>T		intron_variant	Intron 1 of 1	4
LINC00578	ENST00000442937.6	n.289+25738C>T		intron_variant	Intron 2 of 3	3
LINC00578	ENST00000656037.1	n.185-64186C>T		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.329 AC: 49897 AN: 151674 Hom.: 8544 Cov.: 30

Gnomad AFR AF: 0.394

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.507

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.230

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.292

Gnomad OTH AF: 0.293

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

GnomAD4 genome AF: 0.329 AC: 49918 AN: 151792 Hom.: 8540 Cov.: 30 AF XY: 0.327 AC XY: 24273 AN XY: 74156

African (AFR) AF: 0.393 AC: 16270 AN: 41358

American (AMR) AF: 0.336 AC: 5120 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.275 AC: 953 AN: 3464

East Asian (EAS) AF: 0.506 AC: 2607 AN: 5152

South Asian (SAS) AF: 0.361 AC: 1732 AN: 4802

European-Finnish (FIN) AF: 0.230 AC: 2423 AN: 10526

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.292 AC: 19813 AN: 67936

Other (OTH) AF: 0.293 AC: 614 AN: 2096

Alfa AF: 0.299 Hom.: 2927

Bravo AF: 0.338

Asia WGS AF: 0.437 AC: 1517 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.020
DANN	Benign	0.45
PhyloP100		-3.1

Splicing

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

Other links and lift over

dbSNP: rs6443468; hg19: chr3-177283019;