20-22069865-A-G

Variant names:

• chr20-22069865-A-G
• rs1160312
• ENST00000449427.3:n.461+1177A>G

Variant summary

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

The ENST00000449427.3(LINC01432):​n.461+1177A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.554 in 151,692 control chromosomes in the GnomAD database, including 24,371 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 0.55 (24371 hom., cov: 30)
• Consequence: LINC01432 ENST00000449427.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.34
• Publications: 37 publications found

Genes affected

LINC01432 (HGNC:50745): (long intergenic non-protein coding RNA 1432)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.695 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01432	NR_038394.1	n.445+1177A>G		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01432	ENST00000449427.3	n.461+1177A>G		intron_variant	Intron 2 of 3	1
LINC01432	ENST00000793534.1	n.225-3523A>G		intron_variant	Intron 1 of 2
LINC01432	ENST00000793535.1	n.447+1187A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.554 AC: 83977 AN: 151572 Hom.: 24317 Cov.: 30

Gnomad AFR AF: 0.702

Gnomad AMI AF: 0.533

Gnomad AMR AF: 0.646

Gnomad ASJ AF: 0.535

Gnomad EAS AF: 0.684

Gnomad SAS AF: 0.524

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.618

Gnomad NFE AF: 0.469

Gnomad OTH AF: 0.559

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

GnomAD4 genome AF: 0.554 AC: 84096 AN: 151692 Hom.: 24371 Cov.: 30 AF XY: 0.549 AC XY: 40715 AN XY: 74096

African (AFR) AF: 0.702 AC: 29038 AN: 41366

American (AMR) AF: 0.647 AC: 9855 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.535 AC: 1854 AN: 3464

East Asian (EAS) AF: 0.683 AC: 3473 AN: 5082

South Asian (SAS) AF: 0.524 AC: 2515 AN: 4798

European-Finnish (FIN) AF: 0.345 AC: 3630 AN: 10530

Middle Eastern (MID) AF: 0.613 AC: 179 AN: 292

European-Non Finnish (NFE) AF: 0.469 AC: 31880 AN: 67912

Other (OTH) AF: 0.565 AC: 1188 AN: 2102

Alfa AF: 0.504 Hom.: 84243

Bravo AF: 0.586

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.0020
DANN	Benign	0.63
PhyloP100		-3.3

Splicing

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

Other links and lift over

dbSNP: rs1160312; hg19: chr20-22050503;