12-11548554-A-G

Variant names:

• chr12-11548554-A-G
• rs2416791
• ENST00000499291.6:n.331+194A>G

Variant summary

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

The ENST00000499291.6(LINC01252):​n.331+194A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.67 in 152,122 control chromosomes in the GnomAD database, including 41,419 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 0.67 (41419 hom., cov: 31)
• Consequence: LINC01252 ENST00000499291.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.25
• Publications: 20 publications found

Genes affected

LINC01252 (HGNC:27888): (long intergenic non-protein coding RNA 1252)

ENSG00000256237 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.879 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000499291.6. 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
	LINC01252	NR_033890.1		n.331+194A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01252	ENST00000499291.6	TSL:1	n.331+194A>G		intron	N/A
	ENSG00000256237	ENST00000536492.2	TSL:3	n.478-7028T>C		intron	N/A
	LINC01252	ENST00000824801.1		n.151-1036A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.670 AC: 101917 AN: 152004 Hom.: 41432 Cov.: 31

Gnomad AFR AF: 0.184

Gnomad AMI AF: 0.845

Gnomad AMR AF: 0.685

Gnomad ASJ AF: 0.914

Gnomad EAS AF: 0.722

Gnomad SAS AF: 0.847

Gnomad FIN AF: 0.950

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.885

Gnomad OTH AF: 0.734

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

GnomAD4 genome AF: 0.670 AC: 101903 AN: 152122 Hom.: 41419 Cov.: 31 AF XY: 0.676 AC XY: 50277 AN XY: 74384

African (AFR) AF: 0.184 AC: 7610 AN: 41468

American (AMR) AF: 0.685 AC: 10461 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.914 AC: 3172 AN: 3470

East Asian (EAS) AF: 0.722 AC: 3735 AN: 5174

South Asian (SAS) AF: 0.847 AC: 4077 AN: 4816

European-Finnish (FIN) AF: 0.950 AC: 10083 AN: 10614

Middle Eastern (MID) AF: 0.847 AC: 249 AN: 294

European-Non Finnish (NFE) AF: 0.885 AC: 60199 AN: 67990

Other (OTH) AF: 0.734 AC: 1548 AN: 2110

Alfa AF: 0.808 Hom.: 175683

Bravo AF: 0.625

Asia WGS AF: 0.763 AC: 2651 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.5
DANN	Benign	0.77
PhyloP100		1.2

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2416791;

hg19: chr12-11701488;