21-44993811-C-A

Position:

• chr21-44993811-C-A

Variant summary

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

The NR_033840.1(LINC00163):​n.183+93G>T 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 0.186 in 147,684 control chromosomes in the GnomAD database, including 2,624 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 0.19 (2592 hom., cov: 32)
  • Exomes 𝑓: 0.060 (32 hom.)
• Consequence: LINC00163 NR_033840.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43

Genes affected

LINC00163 (HGNC:33165): (long intergenic non-protein coding RNA 163)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.239 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC00163	NR_033840.1	n.183+93G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00163	ENST00000434081.1	n.183+93G>T		intron_variant, non_coding_transcript_variant		1
LINC00163	ENST00000439088.1	n.166+93G>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.189 AC: 27222 AN: 143968 Hom.: 2592 Cov.: 32

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.245

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.132

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.181

GnomAD4 exome AF: 0.0601 AC: 218 AN: 3626 Hom.: 32 AF XY: 0.0649 AC XY: 151 AN XY: 2326

Gnomad4 AFR exome AF: 0.0313

Gnomad4 AMR exome AF: 0.125

Gnomad4 ASJ exome AF: 0.0625

Gnomad4 EAS exome AF: 0.0278

Gnomad4 SAS exome AF: 0.0236

Gnomad4 FIN exome AF: 0.00917

Gnomad4 NFE exome AF: 0.0832

Gnomad4 OTH exome AF: 0.0604

GnomAD4 genome AF: 0.189 AC: 27229 AN: 144058 Hom.: 2592 Cov.: 32 AF XY: 0.188 AC XY: 13307 AN XY: 70710

Gnomad4 AFR AF: 0.152

Gnomad4 AMR AF: 0.245

Gnomad4 ASJ AF: 0.239

Gnomad4 EAS AF: 0.169

Gnomad4 SAS AF: 0.116

Gnomad4 FIN AF: 0.178

Gnomad4 NFE AF: 0.202

Gnomad4 OTH AF: 0.184

Alfa AF: 0.194 Hom.: 361

Bravo AF: 0.187

Asia WGS AF: 0.158 AC: 548 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs36221776; hg19: chr21-46413726;