20-22069865-A-G

Variant summary

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

The NR_038394.1(LINC01432):n.445+1177A>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 0.554 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 NR_038394.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.34

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC01432	NR_038394.1	n.445+1177A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01432	ENST00000449427.3	n.461+1177A>G		intron_variant, non_coding_transcript_variant		1

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

Gnomad4 AFR AF: 0.702

Gnomad4 AMR AF: 0.647

Gnomad4 ASJ AF: 0.535

Gnomad4 EAS AF: 0.683

Gnomad4 SAS AF: 0.524

Gnomad4 FIN AF: 0.345

Gnomad4 NFE AF: 0.469

Gnomad4 OTH AF: 0.565

Alfa AF: 0.502 Hom.: 37923

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1160312; hg19: chr20-22050503;