rs7171889

Positions:

• chr15-94032953-T-G

Variant summary

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

The NR_120320.1(LINC01581):​n.1142-31194A>C 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 0.0695 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 NR_120320.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0610

Genes affected

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

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC01581	NR_120320.1	n.1142-31194A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01581	ENST00000558874.1	n.1142-31194A>C		intron_variant, non_coding_transcript_variant		1
LINC01579	ENST00000556447.5	n.409-2552A>C		intron_variant, non_coding_transcript_variant		4
LINC01579	ENST00000556928.5	n.63-2552A>C		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.0491

Gnomad4 AMR AF: 0.0750

Gnomad4 ASJ AF: 0.0703

Gnomad4 EAS AF: 0.0304

Gnomad4 SAS AF: 0.0661

Gnomad4 FIN AF: 0.0989

Gnomad4 NFE AF: 0.0794

Gnomad4 OTH AF: 0.0748

Alfa AF: 0.0745 Hom.: 612

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7171889; hg19: chr15-94576182;