rs9284813

chr3-87103019-A-G

Variant summary

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

The NR_104153.1(LINC00506):n.328+13412A>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 0.222 in 152,072 control chromosomes in the GnomAD database, including 5,001 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 0.22 (5001 hom., cov: 32)
• Consequence: LINC00506 NR_104153.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.658

Genes affected

LINC00506 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.411 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00506	NR_104153.1	n.328+13412A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00506	ENST00000630120.2	n.402+13412A>G		intron_variant, non_coding_transcript_variant		4
LINC00506	ENST00000628435.1	n.305+13412A>G		intron_variant, non_coding_transcript_variant		4
LINC00506	ENST00000629052.1	n.479+13412A>G		intron_variant, non_coding_transcript_variant		4
LINC00506	ENST00000656042.1	n.331+13412A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.222 AC: 33745 AN: 151954 Hom.: 4996 Cov.: 32

Gnomad AFR AF: 0.416

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.283

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.232

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

GnomAD4 genome AF: 0.222 AC: 33773 AN: 152072 Hom.: 5001 Cov.: 32 AF XY: 0.218 AC XY: 16244 AN XY: 74346

Gnomad4 AFR AF: 0.416

Gnomad4 AMR AF: 0.168

Gnomad4 ASJ AF: 0.282

Gnomad4 EAS AF: 0.241

Gnomad4 SAS AF: 0.157

Gnomad4 FIN AF: 0.107

Gnomad4 NFE AF: 0.135

Gnomad4 OTH AF: 0.231

Alfa AF: 0.157 Hom.: 3804

Bravo AF: 0.239

Asia WGS AF: 0.224 AC: 775 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	4.5
Dann	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9284813; hg19: chr3-87152169; COSMIC: COSV53316856;