14-44199747-T-C

Position:

• chr14-44199747-T-C

Variant summary

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

The ENST00000654351.1(LINC02307):​n.172-150240A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.721 in 142,846 control chromosomes in the GnomAD database, including 37,821 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 0.72 (37821 hom., cov: 21)
• Consequence: LINC02307 ENST00000654351.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.417

Genes affected

LINC02307 (HGNC:53226): (long intergenic non-protein coding RNA 2307)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.948 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02307	ENST00000654351.1	n.172-150240A>G		intron_variant, non_coding_transcript_variant
LINC02307	ENST00000553827.1	n.70-150240A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.720 AC: 102830 AN: 142728 Hom.: 37756 Cov.: 21

Gnomad AFR AF: 0.832

Gnomad AMI AF: 0.759

Gnomad AMR AF: 0.737

Gnomad ASJ AF: 0.674

Gnomad EAS AF: 0.972

Gnomad SAS AF: 0.683

Gnomad FIN AF: 0.668

Gnomad MID AF: 0.648

Gnomad NFE AF: 0.647

Gnomad OTH AF: 0.698

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

GnomAD4 genome AF: 0.721 AC: 102954 AN: 142846 Hom.: 37821 Cov.: 21 AF XY: 0.723 AC XY: 50022 AN XY: 69222

Gnomad4 AFR AF: 0.833

Gnomad4 AMR AF: 0.738

Gnomad4 ASJ AF: 0.674

Gnomad4 EAS AF: 0.972

Gnomad4 SAS AF: 0.682

Gnomad4 FIN AF: 0.668

Gnomad4 NFE AF: 0.647

Gnomad4 OTH AF: 0.701

Alfa AF: 0.691 Hom.: 3842

Bravo AF: 0.740

Asia WGS AF: 0.828 AC: 2852 AN: 3446

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1953479; hg19: chr14-44668950;