chr12-11548554-A-G

Position:

• chr12-11548554-A-G

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LINC01252 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01252	NR_033890.1	n.331+194A>G		intron_variant
LOC124902877	XR_007063210.1	n.279-7028T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01252	ENST00000499291.6	n.331+194A>G		intron_variant		1
ENSG00000256237	ENST00000536492.1	n.57-7028T>C		intron_variant		3

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

Gnomad4 AFR AF: 0.184

Gnomad4 AMR AF: 0.685

Gnomad4 ASJ AF: 0.914

Gnomad4 EAS AF: 0.722

Gnomad4 SAS AF: 0.847

Gnomad4 FIN AF: 0.950

Gnomad4 NFE AF: 0.885

Gnomad4 OTH AF: 0.734

Alfa AF: 0.840 Hom.: 80026

Bravo AF: 0.625

Asia WGS AF: 0.763 AC: 2651 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2416791; hg19: chr12-11701488;