rs7654559

Positions:

• chr4-96389644-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.93-61848T>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 0.232 in 152,116 control chromosomes in the GnomAD database, including 4,295 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 0.23 (4295 hom., cov: 33)
• Consequence: LINC02267 NR_147149.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.547

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 (AFR) allele frequency at 95% confidence interval = 0.265 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02267	NR_147149.1	n.93-61848T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02267	ENST00000522173.1	n.64-61848T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35270 AN: 151998 Hom.: 4298 Cov.: 33

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.327

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.357

Gnomad EAS AF: 0.0173

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.232 AC: 35285 AN: 152116 Hom.: 4295 Cov.: 33 AF XY: 0.228 AC XY: 16972 AN XY: 74382

Gnomad4 AFR AF: 0.270

Gnomad4 AMR AF: 0.186

Gnomad4 ASJ AF: 0.357

Gnomad4 EAS AF: 0.0176

Gnomad4 SAS AF: 0.226

Gnomad4 FIN AF: 0.180

Gnomad4 NFE AF: 0.236

Gnomad4 OTH AF: 0.235

Alfa AF: 0.239 Hom.: 556

Bravo AF: 0.232

Asia WGS AF: 0.138 AC: 480 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.0
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7654559; hg19: chr4-97310795;