rs644695

chr3-177573909-A-G

Variant summary

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

The NR_047568.1(LINC00578):n.289+34416A>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 0.101 in 152,262 control chromosomes in the GnomAD database, including 942 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 0.10 (942 hom., cov: 32)
• Consequence: LINC00578 NR_047568.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0430

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=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.145 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00578	NR_047568.1	n.289+34416A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00578	ENST00000656037.1	n.185-55508A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.102 AC: 15455 AN: 152144 Hom.: 943 Cov.: 32

Gnomad AFR AF: 0.0267

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.0313

Gnomad SAS AF: 0.0957

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.101 AC: 15449 AN: 152262 Hom.: 942 Cov.: 32 AF XY: 0.0997 AC XY: 7423 AN XY: 74448

Gnomad4 AFR AF: 0.0266

Gnomad4 AMR AF: 0.108

Gnomad4 ASJ AF: 0.148

Gnomad4 EAS AF: 0.0313

Gnomad4 SAS AF: 0.0966

Gnomad4 FIN AF: 0.102

Gnomad4 NFE AF: 0.147

Gnomad4 OTH AF: 0.136

Alfa AF: 0.137 Hom.: 1895

Bravo AF: 0.0994

Asia WGS AF: 0.0620 AC: 216 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	1.9
Dann	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs644695; hg19: chr3-177291697;