rs10988341

Variant names:

• chr9-129352900-A-G
• rs10988341
• ENST00000423122.2:n.420-2558A>G

Variant summary

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

The ENST00000423122.2(LINC01503):​n.420-2558A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0352 in 151,972 control chromosomes in the GnomAD database, including 166 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 0.035 (166 hom., cov: 32)
• Consequence: LINC01503 ENST00000423122.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54

Genes affected

LINC01503 (HGNC:51184): (long intergenic non-protein coding RNA 1503)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.148 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
LINC01503	ENST00000423122.2	n.420-2558A>G		intron_variant	Intron 1 of 2	2
LINC01503	ENST00000657393.1	n.658-2558A>G		intron_variant	Intron 2 of 3
LINC01503	ENST00000657651.2	n.557-2558A>G		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.0352 AC: 5348 AN: 151854 Hom.: 165 Cov.: 32

Gnomad AFR AF: 0.00832

Gnomad AMI AF: 0.00879

Gnomad AMR AF: 0.0244

Gnomad ASJ AF: 0.0418

Gnomad EAS AF: 0.157

Gnomad SAS AF: 0.0942

Gnomad FIN AF: 0.0286

Gnomad MID AF: 0.0510

Gnomad NFE AF: 0.0415

Gnomad OTH AF: 0.0360

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

GnomAD4 genome AF: 0.0352 AC: 5345 AN: 151972 Hom.: 166 Cov.: 32 AF XY: 0.0361 AC XY: 2682 AN XY: 74274

Gnomad4 AFR AF: 0.00830

Gnomad4 AMR AF: 0.0244

Gnomad4 ASJ AF: 0.0418

Gnomad4 EAS AF: 0.157

Gnomad4 SAS AF: 0.0943

Gnomad4 FIN AF: 0.0286

Gnomad4 NFE AF: 0.0415

Gnomad4 OTH AF: 0.0361

Alfa AF: 0.0419 Hom.: 219

Bravo AF: 0.0325

Asia WGS AF: 0.109 AC: 379 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.8
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10988341; hg19: chr9-132115179;