2-14226350-A-G

Variant names:

• chr2-14226350-A-G
• rs10495634
• ENST00000417751.5:n.256+90619T>C

Variant summary

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

The ENST00000417751.5(LINC00276):​n.256+90619T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.406 in 151,852 control chromosomes in the GnomAD database, including 12,988 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 (12988 hom., cov: 32)
• Consequence: LINC00276 ENST00000417751.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0210

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=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) 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.256+90619T>C		intron_variant	Intron 2 of 4	2

Frequencies

GnomAD3 genomes AF: 0.406 AC: 61652 AN: 151734 Hom.: 12982 Cov.: 32

Gnomad AFR AF: 0.409

Gnomad AMI AF: 0.529

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.391

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.407

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.447

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.406 AC: 61684 AN: 151852 Hom.: 12988 Cov.: 32 AF XY: 0.399 AC XY: 29572 AN XY: 74186

Gnomad4 AFR AF: 0.409

Gnomad4 AMR AF: 0.324

Gnomad4 ASJ AF: 0.391

Gnomad4 EAS AF: 0.168

Gnomad4 SAS AF: 0.289

Gnomad4 FIN AF: 0.407

Gnomad4 NFE AF: 0.447

Gnomad4 OTH AF: 0.430

Alfa AF: 0.400 Hom.: 3865

Bravo AF: 0.397

Asia WGS AF: 0.255 AC: 887 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.2
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10495634; hg19: chr2-14366474;