rs650258

chr11-61064810-T-C

Variant summary

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

The ENST00000664141.1(LINC02954):n.568-2621T>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 0.669 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 ENST00000664141.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.24

Genes affected

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

LOC105369325 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC105369325	XR_950154.3	n.62+27487A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02954	ENST00000664141.1	n.568-2621T>C		intron_variant, non_coding_transcript_variant
LINC02954	ENST00000536495.1	n.348-2621T>C		intron_variant, non_coding_transcript_variant		3
LINC02954	ENST00000659437.1	n.372-2621T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.657

Gnomad4 AMR AF: 0.708

Gnomad4 ASJ AF: 0.703

Gnomad4 EAS AF: 0.879

Gnomad4 SAS AF: 0.752

Gnomad4 FIN AF: 0.724

Gnomad4 NFE AF: 0.636

Gnomad4 OTH AF: 0.646

Alfa AF: 0.644 Hom.: 44119

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs650258; hg19: chr11-60832282;