11-22474672-C-G

Position:

• chr11-22474672-C-G

Variant summary

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

The NR_120583.1(LINC01495):​n.242+5401G>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 0.536 in 151,558 control chromosomes in the GnomAD database, including 23,962 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 0.54 (23962 hom., cov: 31)
• Consequence: LINC01495 NR_120583.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.125

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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.701 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01495	NR_120583.1	n.242+5401G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01495	ENST00000653021.1	n.296+5401G>C		intron_variant, non_coding_transcript_variant
LINC01495	ENST00000532380.2	n.270+5401G>C		intron_variant, non_coding_transcript_variant		2
LINC01495	ENST00000534135.6	n.270+5401G>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.536 AC: 81144 AN: 151442 Hom.: 23954 Cov.: 31

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.682

Gnomad AMR AF: 0.646

Gnomad ASJ AF: 0.528

Gnomad EAS AF: 0.720

Gnomad SAS AF: 0.578

Gnomad FIN AF: 0.684

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.636

Gnomad OTH AF: 0.558

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

GnomAD4 genome AF: 0.536 AC: 81176 AN: 151558 Hom.: 23962 Cov.: 31 AF XY: 0.542 AC XY: 40137 AN XY: 74034

Gnomad4 AFR AF: 0.261

Gnomad4 AMR AF: 0.646

Gnomad4 ASJ AF: 0.528

Gnomad4 EAS AF: 0.720

Gnomad4 SAS AF: 0.579

Gnomad4 FIN AF: 0.684

Gnomad4 NFE AF: 0.636

Gnomad4 OTH AF: 0.554

Alfa AF: 0.488 Hom.: 1697

Bravo AF: 0.520

Asia WGS AF: 0.585 AC: 2036 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.8
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs340989; hg19: chr11-22496218;