14-44264601-A-G

Position:

• chr14-44264601-A-G

Variant summary

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

The ENST00000553827.1(LINC02307):​n.69+119876T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.818 in 151,090 control chromosomes in the GnomAD database, including 50,667 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 0.82 (50667 hom., cov: 26)
• Consequence: LINC02307 ENST00000553827.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.308

Genes affected

LINC02307 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.956 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02307	NR_187192.1	n.168+121293T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02307	ENST00000553827.1	n.69+119876T>C		intron_variant		3
LINC02307	ENST00000654351.1	n.171+121293T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.818 AC: 123542 AN: 150972 Hom.: 50638 Cov.: 26

Gnomad AFR AF: 0.796

Gnomad AMI AF: 0.854

Gnomad AMR AF: 0.837

Gnomad ASJ AF: 0.797

Gnomad EAS AF: 0.978

Gnomad SAS AF: 0.818

Gnomad FIN AF: 0.871

Gnomad MID AF: 0.729

Gnomad NFE AF: 0.808

Gnomad OTH AF: 0.819

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

GnomAD4 genome AF: 0.818 AC: 123629 AN: 151090 Hom.: 50667 Cov.: 26 AF XY: 0.822 AC XY: 60605 AN XY: 73734

Gnomad4 AFR AF: 0.796

Gnomad4 AMR AF: 0.837

Gnomad4 ASJ AF: 0.797

Gnomad4 EAS AF: 0.978

Gnomad4 SAS AF: 0.817

Gnomad4 FIN AF: 0.871

Gnomad4 NFE AF: 0.808

Gnomad4 OTH AF: 0.820

Alfa AF: 0.812 Hom.: 30700

Bravo AF: 0.816

Asia WGS AF: 0.900 AC: 3129 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8021486; hg19: chr14-44733804;