14-44638258-C-G

Variant names:

• chr14-44638258-C-G
• rs2415872
• ENST00000795537.1:n.153+10587G>C

Variant summary

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

The ENST00000795537.1(LINC02277):​n.153+10587G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.55 in 148,022 control chromosomes in the GnomAD database, including 22,938 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 0.55 (22938 hom., cov: 24)
• Consequence: LINC02277 ENST00000795537.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.668
• Publications: 4 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 (AFR) allele frequency at 95% confidence interval = 0.649 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	ENST00000795537.1	n.153+10587G>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.550 AC: 81293 AN: 147904 Hom.: 22900 Cov.: 24

Gnomad AFR AF: 0.655

Gnomad AMI AF: 0.473

Gnomad AMR AF: 0.514

Gnomad ASJ AF: 0.470

Gnomad EAS AF: 0.590

Gnomad SAS AF: 0.580

Gnomad FIN AF: 0.472

Gnomad MID AF: 0.567

Gnomad NFE AF: 0.507

Gnomad OTH AF: 0.546

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

GnomAD4 genome AF: 0.550 AC: 81381 AN: 148022 Hom.: 22938 Cov.: 24 AF XY: 0.548 AC XY: 39438 AN XY: 71974

African (AFR) AF: 0.656 AC: 26199 AN: 39964

American (AMR) AF: 0.514 AC: 7486 AN: 14570

Ashkenazi Jewish (ASJ) AF: 0.470 AC: 1602 AN: 3410

East Asian (EAS) AF: 0.590 AC: 2974 AN: 5042

South Asian (SAS) AF: 0.580 AC: 2573 AN: 4440

European-Finnish (FIN) AF: 0.472 AC: 4799 AN: 10168

Middle Eastern (MID) AF: 0.565 AC: 165 AN: 292

European-Non Finnish (NFE) AF: 0.507 AC: 34045 AN: 67210

Other (OTH) AF: 0.549 AC: 1111 AN: 2024

Alfa AF: 0.373 Hom.: 916

Bravo AF: 0.561

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.60
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs2415872; hg19: chr14-45107461; COSMIC: COSV53414563;