11-22459887-T-C

Position:

• chr11-22459887-T-C

Variant summary

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

The NR_120583.1(LINC01495):​n.341+7960A>G 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 0.172 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 NR_120583.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.323

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01495	NR_120583.1	n.341+7960A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01495	ENST00000653021.1	n.297-14120A>G		intron_variant, non_coding_transcript_variant
LINC01495	ENST00000532380.2	n.369+7960A>G		intron_variant, non_coding_transcript_variant		2
LINC01495	ENST00000534135.6	n.369+7960A>G		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.0571

Gnomad4 AMR AF: 0.271

Gnomad4 ASJ AF: 0.143

Gnomad4 EAS AF: 0.252

Gnomad4 SAS AF: 0.196

Gnomad4 FIN AF: 0.194

Gnomad4 NFE AF: 0.210

Gnomad4 OTH AF: 0.169

Alfa AF: 0.188 Hom.: 405

Bravo AF: 0.173

Asia WGS AF: 0.216 AC: 751 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10500929; hg19: chr11-22481433;