21-44990632-C-T

Variant names:

• chr21-44990632-C-T
• rs11088977
• ENST00000434081.1:n.1387G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC00163	NR_033840.1	n.1387G>A		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00163	ENST00000434081.1	n.1387G>A		non_coding_transcript_exon_variant	Exon 2 of 2	1
LINC00163	ENST00000439088.1	n.1367G>A		non_coding_transcript_exon_variant	Exon 2 of 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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.500 AC: 1 AN: 2

European-Finnish (FIN) AF: 0.333 AC: 2 AN: 6

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.726 AC: 45 AN: 62

Other (OTH) AF: 0.375 AC: 3 AN: 8

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

African (AFR) AF: 0.202 AC: 8400 AN: 41496

American (AMR) AF: 0.513 AC: 7849 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.523 AC: 1817 AN: 3472

East Asian (EAS) AF: 0.660 AC: 3414 AN: 5172

South Asian (SAS) AF: 0.707 AC: 3410 AN: 4826

European-Finnish (FIN) AF: 0.609 AC: 6453 AN: 10596

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.580 AC: 39449 AN: 67980

Other (OTH) AF: 0.509 AC: 1075 AN: 2110

Alfa AF: 0.533 Hom.: 9366

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
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs11088977; hg19: chr21-46410547;