rs10444671

chr14-44312837-G-C

Variant summary

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

The ENST00000654351.1(LINC02307):n.171+73057C>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 0.142 in 152,068 control chromosomes in the GnomAD database, including 1,678 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 0.14 (1678 hom., cov: 32)
• Consequence: LINC02307 ENST00000654351.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.137

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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.168 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.171+73057C>G		intron_variant, non_coding_transcript_variant
LINC02307	ENST00000553827.1	n.69+71640C>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.142 AC: 21540 AN: 151950 Hom.: 1676 Cov.: 32

Gnomad AFR AF: 0.0934

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.0906

Gnomad SAS AF: 0.0725

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.142 AC: 21558 AN: 152068 Hom.: 1678 Cov.: 32 AF XY: 0.143 AC XY: 10593 AN XY: 74334

Gnomad4 AFR AF: 0.0936

Gnomad4 AMR AF: 0.117

Gnomad4 ASJ AF: 0.151

Gnomad4 EAS AF: 0.0912

Gnomad4 SAS AF: 0.0726

Gnomad4 FIN AF: 0.216

Gnomad4 NFE AF: 0.171

Gnomad4 OTH AF: 0.160

Alfa AF: 0.148 Hom.: 230

Bravo AF: 0.133

Asia WGS AF: 0.0790 AC: 272 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	2.0
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10444671; hg19: chr14-44782040;