rs17181170

Positions:

• chr3-87124174-G-A

Variant summary

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

The NR_104153.1(LINC00506):​n.329-30164G>A 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 0.385 in 151,638 control chromosomes in the GnomAD database, including 12,411 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 0.38 (12411 hom., cov: 31)
• Consequence: LINC00506 NR_104153.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.226

Genes affected

LINC00506 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.483 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC00506	NR_104153.1	n.329-30164G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00506	ENST00000630120.2	n.403-30164G>A		intron_variant, non_coding_transcript_variant		4
LINC00506	ENST00000628435.1	n.306-12011G>A		intron_variant, non_coding_transcript_variant		4
LINC00506	ENST00000629052.1	n.480-16099G>A		intron_variant, non_coding_transcript_variant		4
LINC00506	ENST00000656042.1	n.332-16099G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.385 AC: 58367 AN: 151518 Hom.: 12409 Cov.: 31

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.556

Gnomad AMR AF: 0.385

Gnomad ASJ AF: 0.418

Gnomad EAS AF: 0.305

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.458

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.378

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

GnomAD4 genome AF: 0.385 AC: 58374 AN: 151638 Hom.: 12411 Cov.: 31 AF XY: 0.382 AC XY: 28295 AN XY: 74086

Gnomad4 AFR AF: 0.207

Gnomad4 AMR AF: 0.385

Gnomad4 ASJ AF: 0.418

Gnomad4 EAS AF: 0.305

Gnomad4 SAS AF: 0.339

Gnomad4 FIN AF: 0.458

Gnomad4 NFE AF: 0.488

Gnomad4 OTH AF: 0.377

Alfa AF: 0.466 Hom.: 31729

Bravo AF: 0.374

Asia WGS AF: 0.319 AC: 1110 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.4
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: rs17181170; hg19: chr3-87173324;