2-19874099-G-T

Position:

• chr2-19874099-G-T

Variant summary

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

The NR_033875.1(LINC00954):​n.799+735G>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 0.406 in 152,062 control chromosomes in the GnomAD database, including 12,737 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 0.41 (12737 hom., cov: 33)
• Consequence: LINC00954 NR_033875.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.319

Genes affected

LINC00954 (HGNC:48668): (long intergenic non-protein coding RNA 954)

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 (AFR) allele frequency at 95% confidence interval = 0.472 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC00954	NR_033875.1	n.799+735G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00954	ENST00000449086.5	n.779+735G>T		intron_variant, non_coding_transcript_variant		1
LINC00954	ENST00000433669.2	n.756+735G>T		intron_variant, non_coding_transcript_variant		2
LINC00954	ENST00000607100.5	n.648+735G>T		intron_variant, non_coding_transcript_variant		2
LINC00954	ENST00000649549.1	n.437+735G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.405 AC: 61601 AN: 151944 Hom.: 12725 Cov.: 33

Gnomad AFR AF: 0.477

Gnomad AMI AF: 0.456

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.420

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.379

Gnomad OTH AF: 0.413

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

GnomAD4 genome AF: 0.406 AC: 61667 AN: 152062 Hom.: 12737 Cov.: 33 AF XY: 0.407 AC XY: 30223 AN XY: 74344

Gnomad4 AFR AF: 0.477

Gnomad4 AMR AF: 0.373

Gnomad4 ASJ AF: 0.379

Gnomad4 EAS AF: 0.421

Gnomad4 SAS AF: 0.417

Gnomad4 FIN AF: 0.332

Gnomad4 NFE AF: 0.379

Gnomad4 OTH AF: 0.415

Alfa AF: 0.386 Hom.: 21224

Bravo AF: 0.407

Asia WGS AF: 0.418 AC: 1454 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	0.55
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11096626; hg19: chr2-20073860;