rs10513753

Variant names:

• chr3-177632217-T-G
• rs10513753
• ENST00000439009.1:n.148-119694T>G

Variant summary

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

The ENST00000442937.6(LINC00578):​n.428+2662T>G 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 152,246 control chromosomes in the GnomAD database, including 951 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 (951 hom., cov: 32)
• Consequence: LINC00578 ENST00000442937.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.49
• 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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.123 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000442937.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00578	NR_047568.1		n.428+2662T>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00578	ENST00000439009.1	TSL:4	n.148-119694T>G		intron	N/A
	LINC00578	ENST00000442937.6	TSL:3	n.428+2662T>G		intron	N/A
	LINC00578	ENST00000445673.1	TSL:3	n.253+2662T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.108 AC: 16487 AN: 152128 Hom.: 951 Cov.: 32

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.0972

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.0451

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.108 AC: 16495 AN: 152246 Hom.: 951 Cov.: 32 AF XY: 0.108 AC XY: 8025 AN XY: 74448

African (AFR) AF: 0.126 AC: 5220 AN: 41536

American (AMR) AF: 0.0971 AC: 1485 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.135 AC: 469 AN: 3472

East Asian (EAS) AF: 0.00231 AC: 12 AN: 5192

South Asian (SAS) AF: 0.0456 AC: 220 AN: 4826

European-Finnish (FIN) AF: 0.148 AC: 1566 AN: 10598

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.104 AC: 7107 AN: 68014

Other (OTH) AF: 0.123 AC: 260 AN: 2108

Alfa AF: 0.106 Hom.: 127

Bravo AF: 0.108

Asia WGS AF: 0.0500 AC: 175 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	10
DANN	Benign	0.52
PhyloP100		1.5

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10513753;

hg19: chr3-177350005;