21-44991770-T-C

Position:

• chr21-44991770-T-C

Variant summary

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

The NR_033840.1(LINC00163):​n.249A>G 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 0.391 in 152,182 control chromosomes in the GnomAD database, including 14,035 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 0.39 (14033 hom., cov: 34)
  • Exomes 𝑓: 1.0 (2 hom.)
• Consequence: LINC00163 NR_033840.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.39

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 (SAS) allele frequency at 95% confidence interval = 0.632 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC00163	NR_033840.1	n.249A>G		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00163	ENST00000434081.1	n.249A>G		non_coding_transcript_exon_variant	2/2	1
LINC00163	ENST00000439088.1	n.229A>G		non_coding_transcript_exon_variant	2/2	1

Frequencies

GnomAD3 genomes AF: 0.391 AC: 59493 AN: 152060 Hom.: 14032 Cov.: 34

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.470

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.632

Gnomad SAS AF: 0.650

Gnomad FIN AF: 0.538

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.482

Gnomad OTH AF: 0.420

GnomAD4 exome AF: 1.00 AC: 4 AN: 4 Hom.: 2 Cov.: 0 AF XY: 1.00 AC XY: 2 AN XY: 2

Gnomad4 NFE exome AF: 1.00

GnomAD4 genome AF: 0.391 AC: 59499 AN: 152178 Hom.: 14033 Cov.: 34 AF XY: 0.400 AC XY: 29774 AN XY: 74384

Gnomad4 AFR AF: 0.120

Gnomad4 AMR AF: 0.443

Gnomad4 ASJ AF: 0.406

Gnomad4 EAS AF: 0.631

Gnomad4 SAS AF: 0.651

Gnomad4 FIN AF: 0.538

Gnomad4 NFE AF: 0.482

Gnomad4 OTH AF: 0.421

Alfa AF: 0.432 Hom.: 1975

Bravo AF: 0.367

Asia WGS AF: 0.592 AC: 2056 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	1.2
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13049130; hg19: chr21-46411685;