chr3-87124174-G-A

Variant names:

• chr3-87124174-G-A
• rs17181170
• ENST00000628435.1:n.306-12011G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000628435.1(LINC00506):​n.306-12011G>A variant causes a intron 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 ENST00000628435.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.226
• Publications: 43 publications found

Genes affected

LINC00506 (HGNC:43557): (long intergenic non-protein coding RNA 506)

ENSG00000300916 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC00506	NR_104153.1	n.329-30164G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00506	ENST00000628435.1	n.306-12011G>A		intron_variant	Intron 1 of 2	4
LINC00506	ENST00000629052.1	n.480-16099G>A		intron_variant	Intron 1 of 1	4
LINC00506	ENST00000630120.3	n.648-30164G>A		intron_variant	Intron 1 of 2	4

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

African (AFR) AF: 0.207 AC: 8558 AN: 41356

American (AMR) AF: 0.385 AC: 5842 AN: 15190

Ashkenazi Jewish (ASJ) AF: 0.418 AC: 1448 AN: 3464

East Asian (EAS) AF: 0.305 AC: 1567 AN: 5134

South Asian (SAS) AF: 0.339 AC: 1633 AN: 4814

European-Finnish (FIN) AF: 0.458 AC: 4822 AN: 10518

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.488 AC: 33100 AN: 67854

Other (OTH) AF: 0.377 AC: 794 AN: 2104

Alfa AF: 0.455 Hom.: 68973

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
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs17181170; hg19: chr3-87173324;