chr21-44990632-C-T

Position:

• chr21-44990632-C-T

Variant summary

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

The ENST00000434081.1(LINC00163):​n.1387G>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 0.477 in 152,230 control chromosomes in the GnomAD database, including 19,706 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 0.48 (19687 hom., cov: 34)
  • Exomes 𝑓: 0.65 (19 hom.)
• Consequence: LINC00163 ENST00000434081.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.28

Genes affected

LINC00163 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.687 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC00163	NR_033840.1	n.1387G>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.1387G>A		non_coding_transcript_exon_variant	2/2	1
LINC00163	ENST00000439088.1	n.1367G>A		non_coding_transcript_exon_variant	2/2	1

Frequencies

GnomAD3 genomes AF: 0.477 AC: 72518 AN: 152034 Hom.: 19692 Cov.: 34

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.546

Gnomad AMR AF: 0.513

Gnomad ASJ AF: 0.523

Gnomad EAS AF: 0.661

Gnomad SAS AF: 0.705

Gnomad FIN AF: 0.609

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.580

Gnomad OTH AF: 0.510

GnomAD4 exome AF: 0.654 AC: 51 AN: 78 Hom.: 19 Cov.: 0 AF XY: 0.630 AC XY: 34 AN XY: 54

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.333

Gnomad4 NFE exome AF: 0.726

Gnomad4 OTH exome AF: 0.375

GnomAD4 genome AF: 0.477 AC: 72534 AN: 152152 Hom.: 19687 Cov.: 34 AF XY: 0.482 AC XY: 35874 AN XY: 74358

Gnomad4 AFR AF: 0.202

Gnomad4 AMR AF: 0.513

Gnomad4 ASJ AF: 0.523

Gnomad4 EAS AF: 0.660

Gnomad4 SAS AF: 0.707

Gnomad4 FIN AF: 0.609

Gnomad4 NFE AF: 0.580

Gnomad4 OTH AF: 0.509

Alfa AF: 0.536 Hom.: 7798

Bravo AF: 0.451

Asia WGS AF: 0.645 AC: 2241 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	3.7
DANN	Benign	0.96

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11088977; hg19: chr21-46410547;