rs9287767

Variant names:

• chr2-14038859-A-G
• rs9287767
• ENST00000417751.5:n.257-197245T>C

Variant summary

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

The ENST00000417751.5(LINC00276):​n.257-197245T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.148 in 152,190 control chromosomes in the GnomAD database, including 4,538 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 0.15 (4538 hom., cov: 32)
• Consequence: LINC00276 ENST00000417751.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.160

Genes affected

LINC00276 (HGNC:38663): (long intergenic non-protein coding RNA 276)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.443 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00276	ENST00000417751.5	n.257-197245T>C		intron_variant	Intron 2 of 4	2

Frequencies

GnomAD3 genomes AF: 0.148 AC: 22474 AN: 152072 Hom.: 4510 Cov.: 32

Gnomad AFR AF: 0.448

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0669

Gnomad ASJ AF: 0.0855

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.00820

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.00882

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.148 AC: 22550 AN: 152190 Hom.: 4538 Cov.: 32 AF XY: 0.146 AC XY: 10890 AN XY: 74426

Gnomad4 AFR AF: 0.449

Gnomad4 AMR AF: 0.0668

Gnomad4 ASJ AF: 0.0855

Gnomad4 EAS AF: 0.209

Gnomad4 SAS AF: 0.118

Gnomad4 FIN AF: 0.00820

Gnomad4 NFE AF: 0.00880

Gnomad4 OTH AF: 0.121

Alfa AF: 0.0559 Hom.: 611

Bravo AF: 0.166

Asia WGS AF: 0.196 AC: 680 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.1
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9287767; hg19: chr2-14178984;