rs7171889

Variant names:

• chr15-94032953-T-G
• rs7171889
• ENST00000558874.1:n.1142-31194A>C

Variant summary

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

The ENST00000558874.1(LINC01581):​n.1142-31194A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0695 in 152,302 control chromosomes in the GnomAD database, including 425 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 0.070 (425 hom., cov: 33)
• Consequence: LINC01581 ENST00000558874.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0610
• Publications: 4 publications found

Genes affected

LINC01581 (HGNC:51415): (long intergenic non-protein coding RNA 1581)

LOC105371032 (HGNC:):

LINC01579 (HGNC:27519): (long intergenic non-protein coding RNA 1579)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0777 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371032		n.94032953T>G		intragenic_variant
LINC01581	NR_120320.1	n.1142-31194A>C		intron_variant	Intron 2 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01581	ENST00000558874.1	n.1142-31194A>C		intron_variant	Intron 2 of 8	1
LINC01579	ENST00000556447.5	n.409-2552A>C		intron_variant	Intron 2 of 3	4
LINC01579	ENST00000556928.5	n.63-2552A>C		intron_variant	Intron 1 of 4	3

Frequencies

GnomAD3 genomes AF: 0.0694 AC: 10562 AN: 152184 Hom.: 423 Cov.: 33

Gnomad AFR AF: 0.0490

Gnomad AMI AF: 0.0614

Gnomad AMR AF: 0.0750

Gnomad ASJ AF: 0.0703

Gnomad EAS AF: 0.0304

Gnomad SAS AF: 0.0650

Gnomad FIN AF: 0.0989

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0794

Gnomad OTH AF: 0.0713

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

GnomAD4 genome AF: 0.0695 AC: 10585 AN: 152302 Hom.: 425 Cov.: 33 AF XY: 0.0696 AC XY: 5184 AN XY: 74476

African (AFR) AF: 0.0491 AC: 2041 AN: 41574

American (AMR) AF: 0.0750 AC: 1147 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0703 AC: 244 AN: 3472

East Asian (EAS) AF: 0.0304 AC: 158 AN: 5192

South Asian (SAS) AF: 0.0661 AC: 319 AN: 4828

European-Finnish (FIN) AF: 0.0989 AC: 1049 AN: 10606

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0794 AC: 5403 AN: 68020

Other (OTH) AF: 0.0748 AC: 158 AN: 2112

Alfa AF: 0.0735 Hom.: 840

Bravo AF: 0.0667

Asia WGS AF: 0.0730 AC: 252 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.6
DANN	Benign	0.46
PhyloP100		-0.061

Splicing

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

Other links and lift over

dbSNP: rs7171889; hg19: chr15-94576182;