rs4815610

chr20-3810545-A-G

Variant summary

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

The NR_109859.1(LINC01730):n.227+531A>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 0.478 in 152,166 control chromosomes in the GnomAD database, including 20,486 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 0.48 (20486 hom., cov: 33)
• Consequence: LINC01730 NR_109859.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.769

Genes affected

LINC01730 (HGNC:52518): (long intergenic non-protein coding RNA 1730)

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 (SAS) allele frequency at 95% confidence interval = 0.613 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01730	NR_109859.1	n.227+531A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01730	ENST00000613868.1	n.364+531A>G		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.478 AC: 72642 AN: 152048 Hom.: 20484 Cov.: 33

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.602

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.528

Gnomad EAS AF: 0.493

Gnomad SAS AF: 0.631

Gnomad FIN AF: 0.676

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.600

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.478 AC: 72664 AN: 152166 Hom.: 20486 Cov.: 33 AF XY: 0.483 AC XY: 35948 AN XY: 74380

Gnomad4 AFR AF: 0.160

Gnomad4 AMR AF: 0.579

Gnomad4 ASJ AF: 0.528

Gnomad4 EAS AF: 0.493

Gnomad4 SAS AF: 0.632

Gnomad4 FIN AF: 0.676

Gnomad4 NFE AF: 0.600

Gnomad4 OTH AF: 0.500

Alfa AF: 0.542 Hom.: 4120

Bravo AF: 0.455

Asia WGS AF: 0.555 AC: 1930 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	3.7
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4815610; hg19: chr20-3791192;