11-61057137-G-T

Variant summary

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

The ENST00000664141.1(LINC02954):n.402+1344G>T 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 0.312 in 151,966 control chromosomes in the GnomAD database, including 7,524 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 0.31 (7524 hom., cov: 32)
• Consequence: LINC02954 ENST00000664141.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0310

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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.325 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105369325	XR_950154.3	n.63-26742C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02954	ENST00000664141.1	n.402+1344G>T		intron_variant, non_coding_transcript_variant
LINC02954	ENST00000536495.1	n.57+1344G>T		intron_variant, non_coding_transcript_variant		3
LINC02954	ENST00000659437.1	n.206+1344G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.312 AC: 47354 AN: 151848 Hom.: 7517 Cov.: 32

Gnomad AFR AF: 0.329

Gnomad AMI AF: 0.395

Gnomad AMR AF: 0.267

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.319

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.312 AC: 47397 AN: 151966 Hom.: 7524 Cov.: 32 AF XY: 0.310 AC XY: 23001 AN XY: 74262

Gnomad4 AFR AF: 0.329

Gnomad4 AMR AF: 0.266

Gnomad4 ASJ AF: 0.252

Gnomad4 EAS AF: 0.286

Gnomad4 SAS AF: 0.333

Gnomad4 FIN AF: 0.276

Gnomad4 NFE AF: 0.319

Gnomad4 OTH AF: 0.330

Alfa AF: 0.312 Hom.: 10549

Bravo AF: 0.314

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.15
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs175110; hg19: chr11-60824609;