20-22061780-A-C

Position:

• chr20-22061780-A-C

Variant summary

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

The NR_038394.1(LINC01432):​n.196-6659A>C 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 0.526 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 NR_038394.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.303

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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.666 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01432	NR_038394.1	n.196-6659A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01432	ENST00000449427.3	n.212-6659A>C		intron_variant, non_coding_transcript_variant		1

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

Gnomad4 AFR AF: 0.600

Gnomad4 AMR AF: 0.640

Gnomad4 ASJ AF: 0.534

Gnomad4 EAS AF: 0.685

Gnomad4 SAS AF: 0.523

Gnomad4 FIN AF: 0.344

Gnomad4 NFE AF: 0.469

Gnomad4 OTH AF: 0.548

Alfa AF: 0.510 Hom.: 4301

Bravo AF: 0.554

Asia WGS AF: 0.619 AC: 2152 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs913063; hg19: chr20-22042418;