ENST00000536495.1:n.348-1279A>G

Variant names:

• chr11-61066152-A-G
• rs175126
• ENST00000536495.1:n.348-1279A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000536495.1(LINC02954):​n.348-1279A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.522 in 152,096 control chromosomes in the GnomAD database, including 21,219 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 0.52 (21219 hom., cov: 33)
• Consequence: LINC02954 ENST00000536495.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.37
• Publications: 14 publications found

Genes affected

LINC02954 (HGNC:55972): (long intergenic non-protein coding RNA 2954)

ENSG00000303405 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.72 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02954	NR_186234.1	n.397-1279A>G		intron_variant	Intron 3 of 3
LOC105369325	NR_188502.1	n.62+26145T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02954	ENST00000536495.1	n.348-1279A>G		intron_variant	Intron 3 of 3	3
LINC02954	ENST00000659437.1	n.372-1279A>G		intron_variant	Intron 3 of 3
LINC02954	ENST00000664141.1	n.568-1279A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.522 AC: 79332 AN: 151978 Hom.: 21202 Cov.: 33

Gnomad AFR AF: 0.553

Gnomad AMI AF: 0.486

Gnomad AMR AF: 0.585

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.739

Gnomad SAS AF: 0.645

Gnomad FIN AF: 0.586

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.487

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

GnomAD4 genome AF: 0.522 AC: 79384 AN: 152096 Hom.: 21219 Cov.: 33 AF XY: 0.531 AC XY: 39457 AN XY: 74342

African (AFR) AF: 0.553 AC: 22920 AN: 41470

American (AMR) AF: 0.586 AC: 8946 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.529 AC: 1835 AN: 3470

East Asian (EAS) AF: 0.739 AC: 3828 AN: 5178

South Asian (SAS) AF: 0.644 AC: 3103 AN: 4818

European-Finnish (FIN) AF: 0.586 AC: 6205 AN: 10580

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.455 AC: 30959 AN: 67992

Other (OTH) AF: 0.483 AC: 1018 AN: 2108

Alfa AF: 0.475 Hom.: 51576

Bravo AF: 0.523

Asia WGS AF: 0.649 AC: 2255 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
CADD	Benign	19
DANN	Benign	0.72
PhyloP100		2.4

Splicing

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

Other links and lift over

dbSNP: rs175126; hg19: chr11-60833624;