chr14-44569164-C-T

Variant names:

• chr14-44569164-C-T
• rs1959364
• ENST00000557721.2:n.107+27745G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000557721.2(LINC02277):​n.107+27745G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.676 in 151,924 control chromosomes in the GnomAD database, including 35,044 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 0.68 (35044 hom., cov: 32)
• Consequence: LINC02277 ENST00000557721.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.22
• Publications: 0 publications found

Genes affected

LINC02277 (HGNC:53193): (long intergenic non-protein coding RNA 2277)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.694 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
LINC02277	ENST00000557721.2	n.107+27745G>A		intron_variant	Intron 1 of 3	2
LINC02277	ENST00000795526.1	n.107+27745G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.676 AC: 102605 AN: 151806 Hom.: 35005 Cov.: 32

Gnomad AFR AF: 0.672

Gnomad AMI AF: 0.732

Gnomad AMR AF: 0.571

Gnomad ASJ AF: 0.567

Gnomad EAS AF: 0.582

Gnomad SAS AF: 0.638

Gnomad FIN AF: 0.793

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.699

Gnomad OTH AF: 0.667

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

GnomAD4 genome AF: 0.676 AC: 102689 AN: 151924 Hom.: 35044 Cov.: 32 AF XY: 0.679 AC XY: 50428 AN XY: 74272

African (AFR) AF: 0.672 AC: 27876 AN: 41454

American (AMR) AF: 0.570 AC: 8707 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.567 AC: 1965 AN: 3468

East Asian (EAS) AF: 0.582 AC: 3001 AN: 5156

South Asian (SAS) AF: 0.637 AC: 3068 AN: 4814

European-Finnish (FIN) AF: 0.793 AC: 8349 AN: 10528

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.699 AC: 47466 AN: 67914

Other (OTH) AF: 0.668 AC: 1405 AN: 2102

Alfa AF: 0.691 Hom.: 7616

Bravo AF: 0.657

Asia WGS AF: 0.642 AC: 2230 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.58
DANN	Benign	0.37
PhyloP100		-3.2

Splicing

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

Other links and lift over

dbSNP: rs1959364; hg19: chr14-45038367;