rs10484231

Variant names:

• chr14-44161292-T-G
• rs10484231
• ENST00000553827.1:n.70-111785A>C

Variant summary

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

The ENST00000553827.1(LINC02307):​n.70-111785A>C variant causes a intron 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 ENST00000553827.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.109
• Publications: 2 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.319 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.169-111785A>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02307	ENST00000553827.1	TSL:3	n.70-111785A>C		intron	N/A
	LINC02307	ENST00000654351.1		n.172-111785A>C		intron	N/A

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

African (AFR) AF: 0.0503 AC: 2089 AN: 41544

American (AMR) AF: 0.251 AC: 3833 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.139 AC: 481 AN: 3468

East Asian (EAS) AF: 0.332 AC: 1712 AN: 5158

South Asian (SAS) AF: 0.125 AC: 602 AN: 4824

European-Finnish (FIN) AF: 0.0856 AC: 908 AN: 10606

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.106 AC: 7230 AN: 67978

Other (OTH) AF: 0.121 AC: 255 AN: 2112

Alfa AF: 0.115 Hom.: 2409

Bravo AF: 0.128

Asia WGS AF: 0.263 AC: 915 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.6
DANN	Benign	0.76
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs10484231; hg19: chr14-44630495;