20-22061780-A-C

Variant names:

• chr20-22061780-A-C
• rs913063
• ENST00000449427.3:n.212-6659A>C

Variant summary

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

The ENST00000449427.3(LINC01432):​n.212-6659A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.526 in 151,870 control chromosomes in the GnomAD database, including 21,565 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 0.53 (21565 hom., cov: 31)
• Consequence: LINC01432 ENST00000449427.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.303
• Publications: 12 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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.666 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000449427.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01432	NR_038394.1		n.196-6659A>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01432	ENST00000449427.3	TSL:1	n.212-6659A>C		intron	N/A
	LINC01432	ENST00000793534.1		n.224+7496A>C		intron	N/A
	LINC01432	ENST00000793535.1		n.208-6659A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.525 AC: 79729 AN: 151752 Hom.: 21527 Cov.: 31

Gnomad AFR AF: 0.600

Gnomad AMI AF: 0.532

Gnomad AMR AF: 0.640

Gnomad ASJ AF: 0.534

Gnomad EAS AF: 0.685

Gnomad SAS AF: 0.523

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.469

Gnomad OTH AF: 0.542

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

GnomAD4 genome AF: 0.526 AC: 79832 AN: 151870 Hom.: 21565 Cov.: 31 AF XY: 0.522 AC XY: 38727 AN XY: 74222

African (AFR) AF: 0.600 AC: 24852 AN: 41418

American (AMR) AF: 0.640 AC: 9763 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.534 AC: 1851 AN: 3464

East Asian (EAS) AF: 0.685 AC: 3522 AN: 5140

South Asian (SAS) AF: 0.523 AC: 2516 AN: 4812

European-Finnish (FIN) AF: 0.344 AC: 3631 AN: 10540

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.469 AC: 31878 AN: 67936

Other (OTH) AF: 0.548 AC: 1157 AN: 2110

Alfa AF: 0.521 Hom.: 5211

Bravo AF: 0.554

Asia WGS AF: 0.619 AC: 2152 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.7
DANN	Benign	0.45
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs913063; hg19: chr20-22042418;