rs10444671

Variant names:

• chr14-44312837-G-C
• rs10444671
• ENST00000553827.1:n.69+71640C>G

Variant summary

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

The ENST00000553827.1(LINC02307):​n.69+71640C>G variant causes a intron 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 ENST00000553827.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.137
• 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=-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 rank	MANE	Protein	UniProt
LINC02307	NR_187192.1	n.168+73057C>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02307	ENST00000553827.1	n.69+71640C>G		intron_variant	Intron 1 of 2	3
LINC02307	ENST00000654351.1	n.171+73057C>G		intron_variant	Intron 1 of 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

African (AFR) AF: 0.0936 AC: 3879 AN: 41460

American (AMR) AF: 0.117 AC: 1790 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.151 AC: 525 AN: 3472

East Asian (EAS) AF: 0.0912 AC: 471 AN: 5166

South Asian (SAS) AF: 0.0726 AC: 350 AN: 4822

European-Finnish (FIN) AF: 0.216 AC: 2282 AN: 10578

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.171 AC: 11608 AN: 67982

Other (OTH) AF: 0.160 AC: 338 AN: 2112

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
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs10444671; hg19: chr14-44782040;