chr3-177586510-C-T

Variant names:

• chr3-177586510-C-T
• rs7620503
• ENST00000439009.1:n.147+144400C>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+144400C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.44 in 151,918 control chromosomes in the GnomAD database, including 15,018 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 0.44 (15018 hom., cov: 32)
• Consequence: LINC00578 ENST00000439009.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.376
• Publications: 17 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.532 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00578	NR_047568.1	n.290-42907C>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+144400C>T		intron_variant	Intron 1 of 1	4
LINC00578	ENST00000442937.6	n.290-42907C>T		intron_variant	Intron 2 of 3	3
LINC00578	ENST00000656037.1	n.185-42907C>T		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.440 AC: 66766 AN: 151800 Hom.: 15007 Cov.: 32

Gnomad AFR AF: 0.538

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.439

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.522

Gnomad SAS AF: 0.434

Gnomad FIN AF: 0.356

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.396

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.440 AC: 66823 AN: 151918 Hom.: 15018 Cov.: 32 AF XY: 0.438 AC XY: 32538 AN XY: 74264

African (AFR) AF: 0.538 AC: 22297 AN: 41436

American (AMR) AF: 0.438 AC: 6689 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.323 AC: 1121 AN: 3466

East Asian (EAS) AF: 0.522 AC: 2696 AN: 5164

South Asian (SAS) AF: 0.432 AC: 2079 AN: 4816

European-Finnish (FIN) AF: 0.356 AC: 3747 AN: 10536

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.396 AC: 26882 AN: 67932

Other (OTH) AF: 0.416 AC: 874 AN: 2102

Alfa AF: 0.415 Hom.: 26706

Bravo AF: 0.448

Asia WGS AF: 0.496 AC: 1725 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.1
DANN	Benign	0.31
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs7620503; hg19: chr3-177304298;