chr14-44199747-T-C

Variant names:

• chr14-44199747-T-C
• rs1953479
• ENST00000553827.1:n.70-150240A>G

Variant summary

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

The ENST00000553827.1(LINC02307):​n.70-150240A>G variant causes a intron 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 ENST00000553827.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.417
• Publications: 1 publications found

Genes affected

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

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 (EAS) allele frequency at 95% confidence interval = 0.948 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000553827.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02307	NR_187192.1		n.169-150240A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02307	ENST00000553827.1	TSL:3	n.70-150240A>G		intron	N/A
	LINC02307	ENST00000654351.1		n.172-150240A>G		intron	N/A

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

African (AFR) AF: 0.833 AC: 31721 AN: 38102

American (AMR) AF: 0.738 AC: 10147 AN: 13758

Ashkenazi Jewish (ASJ) AF: 0.674 AC: 2268 AN: 3364

East Asian (EAS) AF: 0.972 AC: 4726 AN: 4864

South Asian (SAS) AF: 0.682 AC: 2950 AN: 4326

European-Finnish (FIN) AF: 0.668 AC: 6492 AN: 9720

Middle Eastern (MID) AF: 0.649 AC: 187 AN: 288

European-Non Finnish (NFE) AF: 0.647 AC: 42440 AN: 65610

Other (OTH) AF: 0.701 AC: 1354 AN: 1932

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.87
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs1953479; hg19: chr14-44668950;