rs650258

Variant names:

• chr11-61064810-T-C
• rs650258
• ENST00000536495.1:n.348-2621T>C

Variant summary

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

The ENST00000536495.1(LINC02954):​n.348-2621T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.669 in 151,872 control chromosomes in the GnomAD database, including 34,250 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 0.67 (34250 hom., cov: 30)
• Consequence: LINC02954 ENST00000536495.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.24
• Publications: 41 publications found

Genes affected

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

ENSG00000303405 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.858 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02954	NR_186234.1	n.397-2621T>C		intron_variant	Intron 3 of 3
LOC105369325	NR_188502.1	n.62+27487A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02954	ENST00000536495.1	n.348-2621T>C		intron_variant	Intron 3 of 3	3
LINC02954	ENST00000659437.1	n.372-2621T>C		intron_variant	Intron 3 of 3
LINC02954	ENST00000664141.1	n.568-2621T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.669 AC: 101479 AN: 151754 Hom.: 34228 Cov.: 30

Gnomad AFR AF: 0.657

Gnomad AMI AF: 0.624

Gnomad AMR AF: 0.708

Gnomad ASJ AF: 0.703

Gnomad EAS AF: 0.879

Gnomad SAS AF: 0.754

Gnomad FIN AF: 0.724

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.636

Gnomad OTH AF: 0.644

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

GnomAD4 genome AF: 0.669 AC: 101550 AN: 151872 Hom.: 34250 Cov.: 30 AF XY: 0.676 AC XY: 50148 AN XY: 74224

African (AFR) AF: 0.657 AC: 27197 AN: 41366

American (AMR) AF: 0.708 AC: 10817 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.703 AC: 2440 AN: 3472

East Asian (EAS) AF: 0.879 AC: 4544 AN: 5168

South Asian (SAS) AF: 0.752 AC: 3623 AN: 4816

European-Finnish (FIN) AF: 0.724 AC: 7635 AN: 10552

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.636 AC: 43176 AN: 67918

Other (OTH) AF: 0.646 AC: 1363 AN: 2110

Alfa AF: 0.650 Hom.: 113989

Bravo AF: 0.669

Asia WGS AF: 0.803 AC: 2794 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.044
DANN	Benign	0.41
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs650258; hg19: chr11-60832282;