11-22459887-T-C

Variant names:

• chr11-22459887-T-C
• rs10500929
• ENST00000532380.3:n.404+7960A>G

Variant summary

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

The ENST00000532380.3(LINC01495):​n.404+7960A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 152,052 control chromosomes in the GnomAD database, including 2,689 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 0.17 (2689 hom., cov: 32)
• Consequence: LINC01495 ENST00000532380.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.323
• Publications: 2 publications found

Genes affected

LINC01495 (HGNC:51161): (long intergenic non-protein coding RNA 1495)

ENSG00000305797 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.264 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000532380.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01495	NR_120583.1		n.341+7960A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01495	ENST00000532380.3	TSL:2	n.404+7960A>G		intron	N/A
	LINC01495	ENST00000534135.6	TSL:2	n.369+7960A>G		intron	N/A
	LINC01495	ENST00000653021.2		n.306-14120A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.173 AC: 26218 AN: 151932 Hom.: 2687 Cov.: 32

Gnomad AFR AF: 0.0572

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.254

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.105

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.168

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

GnomAD4 genome AF: 0.172 AC: 26218 AN: 152052 Hom.: 2689 Cov.: 32 AF XY: 0.176 AC XY: 13049 AN XY: 74306

African (AFR) AF: 0.0571 AC: 2373 AN: 41538

American (AMR) AF: 0.271 AC: 4139 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.143 AC: 496 AN: 3466

East Asian (EAS) AF: 0.252 AC: 1299 AN: 5146

South Asian (SAS) AF: 0.196 AC: 943 AN: 4822

European-Finnish (FIN) AF: 0.194 AC: 2050 AN: 10578

Middle Eastern (MID) AF: 0.110 AC: 32 AN: 292

European-Non Finnish (NFE) AF: 0.210 AC: 14275 AN: 67932

Other (OTH) AF: 0.169 AC: 357 AN: 2112

Alfa AF: 0.183 Hom.: 405

Bravo AF: 0.173

Asia WGS AF: 0.216 AC: 751 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	8.5
DANN	Benign	0.92
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs10500929; hg19: chr11-22481433;