12-93019265-T-C

Position:

• chr12-93019265-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_040096.1(LOC643339):​n.428-14667A>G variant causes a intron, non coding transcript 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: LOC643339 NR_040096.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.575

Genes affected

(HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LOC643339	NR_040096.1	n.428-14667A>G		intron_variant, non_coding_transcript_variant
LINC02413	XR_945212.3	n.440-146T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000549930.1	n.99-14667A>G		intron_variant, non_coding_transcript_variant		5
LINC02413	ENST00000552353.2	n.489-146T>C		intron_variant, non_coding_transcript_variant		5
	ENST00000550324.6	n.86-14667A>G		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 NFE exome AF: 0.800

Gnomad4 OTH exome AF: 0.750

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

Gnomad4 AFR AF: 0.885

Gnomad4 AMR AF: 0.696

Gnomad4 ASJ AF: 0.735

Gnomad4 EAS AF: 0.593

Gnomad4 SAS AF: 0.692

Gnomad4 FIN AF: 0.613

Gnomad4 NFE AF: 0.609

Gnomad4 OTH AF: 0.698

Alfa AF: 0.631 Hom.: 62774

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3825179; hg19: chr12-93413041;