rs10513753

Positions:

• chr3-177632217-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_047568.1(LINC00578):​n.428+2662T>G variant causes a intron, non coding transcript 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 NR_047568.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.49

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00578	NR_047568.1	n.428+2662T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00578	ENST00000656037.1	n.323+2662T>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.126

Gnomad4 AMR AF: 0.0971

Gnomad4 ASJ AF: 0.135

Gnomad4 EAS AF: 0.00231

Gnomad4 SAS AF: 0.0456

Gnomad4 FIN AF: 0.148

Gnomad4 NFE AF: 0.104

Gnomad4 OTH AF: 0.123

Alfa AF: 0.105 Hom.: 124

Bravo AF: 0.108

Asia WGS AF: 0.0500 AC: 175 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10513753; hg19: chr3-177350005;