chr21-44990442-G-T

Position:

• chr21-44990442-G-T

Variant summary

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

The NR_033840.1(LINC00163):​n.1577C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.18 in 152,360 control chromosomes in the GnomAD database, including 2,627 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 0.18 (2625 hom., cov: 33)
  • Exomes 𝑓: 0.18 (2 hom.)
• Consequence: LINC00163 NR_033840.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365

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=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.236 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC00163	NR_033840.1	n.1577C>A		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00163	ENST00000434081.1	n.1577C>A		non_coding_transcript_exon_variant	2/2	1
LINC00163	ENST00000439088.1	n.1557C>A		non_coding_transcript_exon_variant	2/2	1

Frequencies

GnomAD3 genomes AF: 0.180 AC: 27404 AN: 152052 Hom.: 2627 Cov.: 33

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.179

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.176

GnomAD4 exome AF: 0.181 AC: 34 AN: 188 Hom.: 2 Cov.: 0 AF XY: 0.184 AC XY: 29 AN XY: 158

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.333

Gnomad4 NFE exome AF: 0.198

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.180 AC: 27409 AN: 152172 Hom.: 2625 Cov.: 33 AF XY: 0.181 AC XY: 13457 AN XY: 74404

Gnomad4 AFR AF: 0.133

Gnomad4 AMR AF: 0.243

Gnomad4 ASJ AF: 0.239

Gnomad4 EAS AF: 0.169

Gnomad4 SAS AF: 0.119

Gnomad4 FIN AF: 0.179

Gnomad4 NFE AF: 0.197

Gnomad4 OTH AF: 0.179

Alfa AF: 0.0874 Hom.: 110

Bravo AF: 0.186

Asia WGS AF: 0.158 AC: 550 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.3
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs36221774; hg19: chr21-46410357;