rs10484231

chr14-44161292-T-G

Variant summary

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

The ENST00000654351.1(LINC02307):n.172-111785A>C 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 0.114 in 152,180 control chromosomes in the GnomAD database, including 1,403 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 0.11 (1403 hom., cov: 32)
• Consequence: LINC02307 ENST00000654351.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.109

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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.319 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.172-111785A>C		intron_variant, non_coding_transcript_variant
LINC02307	ENST00000553827.1	n.70-111785A>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.114 AC: 17303 AN: 152064 Hom.: 1386 Cov.: 32

Gnomad AFR AF: 0.0503

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.0856

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.114

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

GnomAD4 genome AF: 0.114 AC: 17342 AN: 152180 Hom.: 1403 Cov.: 32 AF XY: 0.119 AC XY: 8819 AN XY: 74416

Gnomad4 AFR AF: 0.0503

Gnomad4 AMR AF: 0.251

Gnomad4 ASJ AF: 0.139

Gnomad4 EAS AF: 0.332

Gnomad4 SAS AF: 0.125

Gnomad4 FIN AF: 0.0856

Gnomad4 NFE AF: 0.106

Gnomad4 OTH AF: 0.121

Alfa AF: 0.116 Hom.: 1581

Bravo AF: 0.128

Asia WGS AF: 0.263 AC: 915 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	5.6
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10484231; hg19: chr14-44630495;