12-31944426-G-T

Variant names:

• chr12-31944426-G-T
• rs1151008
• ENST00000662662.1:n.189+14702C>A

Variant summary

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

The ENST00000662662.1(LINC02422):​n.189+14702C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.564 in 152,032 control chromosomes in the GnomAD database, including 25,627 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 0.56 (25627 hom., cov: 33)
• Consequence: LINC02422 ENST00000662662.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.137
• Publications: 7 publications found

Genes affected

LINC02422 (HGNC:53352): (long intergenic non-protein coding RNA 2422)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.822 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02422	ENST00000662662.1	n.189+14702C>A		intron_variant	Intron 1 of 2
LINC02422	ENST00000752257.1	n.174+14702C>A		intron_variant	Intron 1 of 2
LINC02422	ENST00000752258.1	n.174+14702C>A		intron_variant	Intron 1 of 2
LINC02422	ENST00000752259.1	n.174+14702C>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.564 AC: 85687 AN: 151914 Hom.: 25622 Cov.: 33

Gnomad AFR AF: 0.369

Gnomad AMI AF: 0.827

Gnomad AMR AF: 0.694

Gnomad ASJ AF: 0.725

Gnomad EAS AF: 0.788

Gnomad SAS AF: 0.845

Gnomad FIN AF: 0.563

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.602

Gnomad OTH AF: 0.619

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

GnomAD4 genome AF: 0.564 AC: 85712 AN: 152032 Hom.: 25627 Cov.: 33 AF XY: 0.574 AC XY: 42634 AN XY: 74302

African (AFR) AF: 0.368 AC: 15269 AN: 41452

American (AMR) AF: 0.695 AC: 10618 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.725 AC: 2515 AN: 3470

East Asian (EAS) AF: 0.788 AC: 4079 AN: 5176

South Asian (SAS) AF: 0.844 AC: 4068 AN: 4820

European-Finnish (FIN) AF: 0.563 AC: 5943 AN: 10552

Middle Eastern (MID) AF: 0.759 AC: 223 AN: 294

European-Non Finnish (NFE) AF: 0.602 AC: 40933 AN: 67968

Other (OTH) AF: 0.621 AC: 1310 AN: 2108

Alfa AF: 0.606 Hom.: 30010

Bravo AF: 0.563

Asia WGS AF: 0.811 AC: 2818 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.5
DANN	Benign	0.74
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs1151008; hg19: chr12-32097360;