12-42616221-A-G

Variant names:

• chr12-42616221-A-G
• rs4590936
• ENST00000550337.2:n.763-259T>C

Variant summary

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

The ENST00000550337.2(LINC02402):​n.763-259T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.844 in 152,124 control chromosomes in the GnomAD database, including 56,277 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 0.84 (56277 hom., cov: 31)
• Consequence: LINC02402 ENST00000550337.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240

Genes affected

LINC02402 (HGNC:53329): (long intergenic non-protein coding RNA 2402)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.947 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02402	NR_110042.1	n.753-259T>C		intron_variant	Intron 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02402	ENST00000550337.2	n.763-259T>C		intron_variant	Intron 5 of 5	1
LINC02402	ENST00000662847.1	n.1493-259T>C		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.845 AC: 128382 AN: 152006 Hom.: 56259 Cov.: 31

Gnomad AFR AF: 0.587

Gnomad AMI AF: 0.939

Gnomad AMR AF: 0.893

Gnomad ASJ AF: 0.905

Gnomad EAS AF: 0.900

Gnomad SAS AF: 0.951

Gnomad FIN AF: 0.975

Gnomad MID AF: 0.915

Gnomad NFE AF: 0.954

Gnomad OTH AF: 0.851

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

GnomAD4 genome AF: 0.844 AC: 128440 AN: 152124 Hom.: 56277 Cov.: 31 AF XY: 0.848 AC XY: 63049 AN XY: 74370

Gnomad4 AFR AF: 0.586

Gnomad4 AMR AF: 0.893

Gnomad4 ASJ AF: 0.905

Gnomad4 EAS AF: 0.900

Gnomad4 SAS AF: 0.951

Gnomad4 FIN AF: 0.975

Gnomad4 NFE AF: 0.953

Gnomad4 OTH AF: 0.853

Alfa AF: 0.899 Hom.: 4040

Bravo AF: 0.825

Asia WGS AF: 0.905 AC: 3145 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.0
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4590936; hg19: chr12-43010023;