4-96312526-T-C

Position:

• chr4-96312526-T-C

Variant summary

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

The NR_147149.1(LINC02267):​n.92+1732T>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 0.405 in 151,658 control chromosomes in the GnomAD database, including 13,312 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 (13312 hom., cov: 31)
• Consequence: LINC02267 NR_147149.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214

Genes affected

LINC02267 (HGNC:53181): (long intergenic non-protein coding RNA 2267)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.61 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02267	NR_147149.1	n.92+1732T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02267	ENST00000522173.1	n.63+1732T>C		intron_variant, non_coding_transcript_variant		3
LINC02267	ENST00000513393.1	n.94+1732T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.405 AC: 61379 AN: 151540 Hom.: 13289 Cov.: 31

Gnomad AFR AF: 0.525

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.461

Gnomad ASJ AF: 0.353

Gnomad EAS AF: 0.628

Gnomad SAS AF: 0.444

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.419

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

GnomAD4 genome AF: 0.405 AC: 61441 AN: 151658 Hom.: 13312 Cov.: 31 AF XY: 0.408 AC XY: 30227 AN XY: 74092

Gnomad4 AFR AF: 0.524

Gnomad4 AMR AF: 0.461

Gnomad4 ASJ AF: 0.353

Gnomad4 EAS AF: 0.628

Gnomad4 SAS AF: 0.444

Gnomad4 FIN AF: 0.348

Gnomad4 NFE AF: 0.314

Gnomad4 OTH AF: 0.418

Alfa AF: 0.307 Hom.: 3285

Bravo AF: 0.419

Asia WGS AF: 0.542 AC: 1886 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.5
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2048022; hg19: chr4-97233677;