rs17023900

Variant names:

• chr3-87085650-A-G
• rs17023900
• ENST00000774840.1:n.508+43943A>G

Variant summary

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

The ENST00000774840.1(LINC00506):​n.508+43943A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0727 in 152,266 control chromosomes in the GnomAD database, including 510 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 0.073 (510 hom., cov: 32)
• Consequence: LINC00506 ENST00000774840.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.816
• Publications: 27 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.113 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00506	ENST00000774840.1	n.508+43943A>G		intron_variant	Intron 3 of 3
LINC00506	ENST00000774841.1	n.454+43943A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.0728 AC: 11070 AN: 152148 Hom.: 511 Cov.: 32

Gnomad AFR AF: 0.0437

Gnomad AMI AF: 0.0614

Gnomad AMR AF: 0.0940

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.0796

Gnomad FIN AF: 0.0366

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.0812

Gnomad OTH AF: 0.0948

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

GnomAD4 genome AF: 0.0727 AC: 11068 AN: 152266 Hom.: 510 Cov.: 32 AF XY: 0.0723 AC XY: 5383 AN XY: 74460

African (AFR) AF: 0.0436 AC: 1813 AN: 41560

American (AMR) AF: 0.0939 AC: 1436 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.171 AC: 593 AN: 3470

East Asian (EAS) AF: 0.121 AC: 626 AN: 5164

South Asian (SAS) AF: 0.0788 AC: 380 AN: 4822

European-Finnish (FIN) AF: 0.0366 AC: 389 AN: 10628

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.0812 AC: 5521 AN: 68012

Other (OTH) AF: 0.0943 AC: 199 AN: 2110

Alfa AF: 0.0807 Hom.: 1653

Bravo AF: 0.0767

Asia WGS AF: 0.118 AC: 410 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	5.9
DANN	Benign	0.25
PhyloP100		0.82

Splicing

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

Other links and lift over

dbSNP: rs17023900; hg19: chr3-87134800;