rs17633881

Variant names:

• chr3-177629101-T-C
• rs17633881
• ENST00000439009.1:n.148-122810T>C

Variant summary

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

The ENST00000439009.1(LINC00578):​n.148-122810T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 152,186 control chromosomes in the GnomAD database, including 953 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 0.11 (953 hom., cov: 32)
• Consequence: LINC00578 ENST00000439009.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.15
• Publications: 5 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=-0.59).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.123 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00578	NR_047568.1	n.290-316T>C		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00578	ENST00000439009.1	n.148-122810T>C		intron_variant	Intron 1 of 1	4
LINC00578	ENST00000442937.6	n.290-316T>C		intron_variant	Intron 2 of 3	3
LINC00578	ENST00000445673.1	n.115-316T>C		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.108 AC: 16484 AN: 152068 Hom.: 953 Cov.: 32

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.0971

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.0487

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.108 AC: 16491 AN: 152186 Hom.: 953 Cov.: 32 AF XY: 0.108 AC XY: 8029 AN XY: 74404

African (AFR) AF: 0.126 AC: 5215 AN: 41510

American (AMR) AF: 0.0970 AC: 1483 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.135 AC: 469 AN: 3470

East Asian (EAS) AF: 0.00231 AC: 12 AN: 5190

South Asian (SAS) AF: 0.0489 AC: 236 AN: 4826

European-Finnish (FIN) AF: 0.148 AC: 1563 AN: 10580

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.104 AC: 7096 AN: 68008

Other (OTH) AF: 0.123 AC: 259 AN: 2110

Alfa AF: 0.110 Hom.: 1586

Bravo AF: 0.108

Asia WGS AF: 0.0510 AC: 178 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	9.4
DANN	Benign	0.94
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs17633881; hg19: chr3-177346889;