rs1561164

Variant names:

• chr3-87076876-G-A
• rs1561164
• ENST00000774840.1:n.508+35169G>A

Variant summary

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

The ENST00000774840.1(LINC00506):​n.508+35169G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0442 in 151,968 control chromosomes in the GnomAD database, including 193 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 0.044 (193 hom., cov: 32)
• Consequence: LINC00506 ENST00000774840.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.453
• Publications: 3 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0844 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+35169G>A		intron_variant	Intron 3 of 3
LINC00506	ENST00000774841.1	n.454+35169G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.0441 AC: 6692 AN: 151850 Hom.: 191 Cov.: 32

Gnomad AFR AF: 0.0865

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0305

Gnomad ASJ AF: 0.0150

Gnomad EAS AF: 0.00462

Gnomad SAS AF: 0.0108

Gnomad FIN AF: 0.0340

Gnomad MID AF: 0.0255

Gnomad NFE AF: 0.0304

Gnomad OTH AF: 0.0436

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

GnomAD4 genome AF: 0.0442 AC: 6713 AN: 151968 Hom.: 193 Cov.: 32 AF XY: 0.0434 AC XY: 3224 AN XY: 74276

African (AFR) AF: 0.0867 AC: 3597 AN: 41466

American (AMR) AF: 0.0306 AC: 467 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.0150 AC: 52 AN: 3466

East Asian (EAS) AF: 0.00463 AC: 24 AN: 5178

South Asian (SAS) AF: 0.0108 AC: 52 AN: 4812

European-Finnish (FIN) AF: 0.0340 AC: 358 AN: 10542

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0304 AC: 2063 AN: 67940

Other (OTH) AF: 0.0431 AC: 91 AN: 2110

Alfa AF: 0.0325 Hom.: 47

Bravo AF: 0.0463

Asia WGS AF: 0.0230 AC: 79 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.36
DANN	Benign	0.40
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs1561164; hg19: chr3-87126026;