21-44991755-G-A

Position:

• chr21-44991755-G-A

Variant summary

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

The NR_033840.1(LINC00163):​n.264C>T 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 0.193 in 152,224 control chromosomes in the GnomAD database, including 2,939 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 (2939 hom., cov: 34)
  • Exomes 𝑓: 0.10 (0 hom.)
• Consequence: LINC00163 NR_033840.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.64

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.241 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00163	NR_033840.1	n.264C>T		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00163	ENST00000434081.1	n.264C>T		non_coding_transcript_exon_variant	2/2	1
LINC00163	ENST00000439088.1	n.244C>T		non_coding_transcript_exon_variant	2/2	1

Frequencies

GnomAD3 genomes AF: 0.193 AC: 29347 AN: 152096 Hom.: 2940 Cov.: 34

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.185

GnomAD4 exome AF: 0.100 AC: 1 AN: 10 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 4

Gnomad4 SAS exome AF: 0.00

Gnomad4 NFE exome AF: 0.125

GnomAD4 genome AF: 0.193 AC: 29351 AN: 152214 Hom.: 2939 Cov.: 34 AF XY: 0.193 AC XY: 14377 AN XY: 74448

Gnomad4 AFR AF: 0.175

Gnomad4 AMR AF: 0.248

Gnomad4 ASJ AF: 0.244

Gnomad4 EAS AF: 0.174

Gnomad4 SAS AF: 0.119

Gnomad4 FIN AF: 0.180

Gnomad4 NFE AF: 0.198

Gnomad4 OTH AF: 0.188

Alfa AF: 0.201 Hom.: 491

Bravo AF: 0.200

Asia WGS AF: 0.159 AC: 554 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.46
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11702692; hg19: chr21-46411670;