2-10881605-T-G

Variant summary

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

The NR_110575.1(LINC01954):n.178+3161T>G 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 0.224 in 152,196 control chromosomes in the GnomAD database, including 4,605 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 0.22 (4605 hom., cov: 33)
• Consequence: LINC01954 NR_110575.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.939

Genes affected

LINC01954 (HGNC:52779): (long intergenic non-protein coding RNA 1954)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.347 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01954	NR_110575.1	n.178+3161T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01954	ENST00000607419.1	n.176+3161T>G		intron_variant, non_coding_transcript_variant		1
LINC01954	ENST00000691398.1	n.283-3229T>G		intron_variant, non_coding_transcript_variant
LINC01954	ENST00000652896.1	n.470-3229T>G		intron_variant, non_coding_transcript_variant
LINC01954	ENST00000670239.2	n.446+3161T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.223 AC: 33951 AN: 152078 Hom.: 4581 Cov.: 33

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.344

Gnomad SAS AF: 0.361

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.224 AC: 34029 AN: 152196 Hom.: 4605 Cov.: 33 AF XY: 0.225 AC XY: 16724 AN XY: 74426

Gnomad4 AFR AF: 0.349

Gnomad4 AMR AF: 0.225

Gnomad4 ASJ AF: 0.185

Gnomad4 EAS AF: 0.344

Gnomad4 SAS AF: 0.361

Gnomad4 FIN AF: 0.117

Gnomad4 NFE AF: 0.147

Gnomad4 OTH AF: 0.227

Alfa AF: 0.152 Hom.: 986

Bravo AF: 0.234

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.29
Dann	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4669638; hg19: chr2-11021731;