rs10520786

Variant names:

• chr15-95486482-C-T
• rs10520786
• ENST00000554837.5:n.338-11199C>T

Variant summary

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

The ENST00000554837.5(LINC00924):​n.338-11199C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0979 in 152,136 control chromosomes in the GnomAD database, including 1,103 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 0.098 (1103 hom., cov: 32)
• Consequence: LINC00924 ENST00000554837.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.240
• Publications: 0 publications found

Genes affected

LINC00924 (HGNC:27081): (long intergenic non-protein coding RNA 924)

ENSG00000258489 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.209 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00924	NR_027132.1	n.340-11199C>T		intron_variant	Intron 3 of 6
LINC00924	NR_027133.1	n.340-11199C>T		intron_variant	Intron 3 of 5
LOC105370993	NR_188325.1	n.185+5017G>A		intron_variant	Intron 2 of 3
LOC105370993	NR_188326.1	n.134+7168G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00924	ENST00000554837.5	n.338-11199C>T		intron_variant	Intron 3 of 5	1
ENSG00000258489	ENST00000554412.3	n.130+7168G>A		intron_variant	Intron 1 of 2	2
LINC00924	ENST00000556053.2	n.338-11199C>T		intron_variant	Intron 3 of 6	2

Frequencies

GnomAD3 genomes AF: 0.0976 AC: 14844 AN: 152018 Hom.: 1091 Cov.: 32

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.0307

Gnomad AMR AF: 0.0540

Gnomad ASJ AF: 0.0784

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0321

Gnomad FIN AF: 0.0427

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0603

Gnomad OTH AF: 0.0905

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

GnomAD4 genome AF: 0.0979 AC: 14890 AN: 152136 Hom.: 1103 Cov.: 32 AF XY: 0.0946 AC XY: 7036 AN XY: 74402

African (AFR) AF: 0.213 AC: 8839 AN: 41470

American (AMR) AF: 0.0539 AC: 824 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0784 AC: 272 AN: 3470

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5182

South Asian (SAS) AF: 0.0325 AC: 157 AN: 4828

European-Finnish (FIN) AF: 0.0427 AC: 453 AN: 10600

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0603 AC: 4099 AN: 67984

Other (OTH) AF: 0.0896 AC: 189 AN: 2110

Alfa AF: 0.0691 Hom.: 917

Bravo AF: 0.102

Asia WGS AF: 0.0290 AC: 99 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.5
DANN	Benign	0.84
PhyloP100		-0.24
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs10520786; hg19: chr15-96029711;