chr12-93019265-T-C

Variant names:

• chr12-93019265-T-C
• rs3825179
• ENST00000549930.1:n.99-14667A>G

Variant summary

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

The ENST00000549930.1(ENSG00000257252):​n.99-14667A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.699 in 152,290 control chromosomes in the GnomAD database, including 38,347 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 0.70 (38340 hom., cov: 33)
  • Exomes 𝑓: 0.79 (7 hom.)
• Consequence: ENSG00000257252 ENST00000549930.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.575
• Publications: 3 publications found

Genes affected

ENSG00000257252 (HGNC:):

LINC02413 (HGNC:53342): (long intergenic non-protein coding RNA 2413)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.877 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC643339	NR_040096.1	n.428-14667A>G		intron_variant	Intron 3 of 4
LINC02413	XR_945212.3	n.440-146T>C		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000257252	ENST00000549930.1	n.99-14667A>G		intron_variant	Intron 1 of 2	5
ENSG00000257252	ENST00000550324.7	n.169-14667A>G		intron_variant	Intron 1 of 2	3
LINC02413	ENST00000552353.2	n.489-146T>C		intron_variant	Intron 3 of 3	5

Frequencies

GnomAD3 genomes AF: 0.699 AC: 106276 AN: 152148 Hom.: 38272 Cov.: 33

Gnomad AFR AF: 0.884

Gnomad AMI AF: 0.476

Gnomad AMR AF: 0.696

Gnomad ASJ AF: 0.735

Gnomad EAS AF: 0.593

Gnomad SAS AF: 0.691

Gnomad FIN AF: 0.613

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.609

Gnomad OTH AF: 0.694

GnomAD4 exome AF: 0.792 AC: 19 AN: 24 Hom.: 7 AF XY: 0.800 AC XY: 16 AN XY: 20

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.800 AC: 16 AN: 20

Other (OTH) AF: 0.750 AC: 3 AN: 4

GnomAD4 genome AF: 0.699 AC: 106405 AN: 152266 Hom.: 38340 Cov.: 33 AF XY: 0.697 AC XY: 51852 AN XY: 74438

African (AFR) AF: 0.885 AC: 36771 AN: 41566

American (AMR) AF: 0.696 AC: 10646 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.735 AC: 2553 AN: 3472

East Asian (EAS) AF: 0.593 AC: 3071 AN: 5180

South Asian (SAS) AF: 0.692 AC: 3345 AN: 4832

European-Finnish (FIN) AF: 0.613 AC: 6499 AN: 10596

Middle Eastern (MID) AF: 0.721 AC: 212 AN: 294

European-Non Finnish (NFE) AF: 0.609 AC: 41396 AN: 68004

Other (OTH) AF: 0.698 AC: 1478 AN: 2116

Alfa AF: 0.641 Hom.: 133806

Bravo AF: 0.711

Asia WGS AF: 0.662 AC: 2303 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.1
DANN	Benign	0.65
PhyloP100		0.57

Splicing

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

Other links and lift over

dbSNP: rs3825179; hg19: chr12-93413041;