chr14-87405491-A-G

Position:

• chr14-87405491-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000557070.1(LINC02296):​n.329+889T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0391 in 152,150 control chromosomes in the GnomAD database, including 124 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 0.039 (124 hom., cov: 32)
• Consequence: LINC02296 ENST00000557070.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.06

Genes affected

LINC02296 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BS1: Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.0391 (5955/152150) while in subpopulation EAS AF= 0.0497 (256/5154). AF 95% confidence interval is 0.0447. There are 124 homozygotes in gnomad4. There are 2900 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 124 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02296	XR_007064293.1	n.3002+889T>C		intron_variant
LINC02296	XR_007064294.1	n.1787+889T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02296	ENST00000557070.1	n.329+889T>C		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.0392 AC: 5956 AN: 152032 Hom.: 124 Cov.: 32

Gnomad AFR AF: 0.0360

Gnomad AMI AF: 0.0186

Gnomad AMR AF: 0.0254

Gnomad ASJ AF: 0.0697

Gnomad EAS AF: 0.0501

Gnomad SAS AF: 0.0290

Gnomad FIN AF: 0.0479

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0413

Gnomad OTH AF: 0.0473

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

GnomAD4 genome AF: 0.0391 AC: 5955 AN: 152150 Hom.: 124 Cov.: 32 AF XY: 0.0390 AC XY: 2900 AN XY: 74396

Gnomad4 AFR AF: 0.0359

Gnomad4 AMR AF: 0.0254

Gnomad4 ASJ AF: 0.0697

Gnomad4 EAS AF: 0.0497

Gnomad4 SAS AF: 0.0292

Gnomad4 FIN AF: 0.0479

Gnomad4 NFE AF: 0.0413

Gnomad4 OTH AF: 0.0459

Alfa AF: 0.0404 Hom.: 177

Bravo AF: 0.0361

Asia WGS AF: 0.0390 AC: 136 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.8
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17741027; hg19: chr14-87871835;