21-44990155-C-T

Variant names:

• chr21-44990155-C-T
• rs36221483
• ENST00000434081.1:n.1864G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000434081.1(LINC00163):​n.1864G>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 0.117 in 152,254 control chromosomes in the GnomAD database, including 1,113 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 0.12 (1113 hom., cov: 33)
  • Exomes 𝑓: 0.19 (0 hom.)
• Consequence: LINC00163 ENST00000434081.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.736
• Publications: 2 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.166 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000434081.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00163	NR_033840.1		n.1864G>A		non_coding_transcript_exon	Exon 2 of 2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00163	ENST00000434081.1	TSL:1	n.1864G>A		non_coding_transcript_exon	Exon 2 of 2
	LINC00163	ENST00000439088.1	TSL:1	n.1844G>A		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17802 AN: 152120 Hom.: 1115 Cov.: 33

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.0387

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.0860

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.103

GnomAD4 exome AF: 0.188 AC: 3 AN: 16 Hom.: 0 Cov.: 0 AF XY: 0.250 AC XY: 3 AN XY: 12

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) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.250 AC: 3 AN: 12

Other (OTH) AF: 0.00 AC: 0 AN: 4

GnomAD4 genome AF: 0.117 AC: 17804 AN: 152238 Hom.: 1113 Cov.: 33 AF XY: 0.119 AC XY: 8824 AN XY: 74418

African (AFR) AF: 0.103 AC: 4300 AN: 41550

American (AMR) AF: 0.171 AC: 2622 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.131 AC: 456 AN: 3470

East Asian (EAS) AF: 0.108 AC: 559 AN: 5162

South Asian (SAS) AF: 0.0383 AC: 185 AN: 4824

European-Finnish (FIN) AF: 0.133 AC: 1415 AN: 10612

Middle Eastern (MID) AF: 0.0788 AC: 23 AN: 292

European-Non Finnish (NFE) AF: 0.116 AC: 7860 AN: 68002

Other (OTH) AF: 0.103 AC: 218 AN: 2114

Alfa AF: 0.0640 Hom.: 70

Bravo AF: 0.121

Asia WGS AF: 0.0850 AC: 296 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.6
DANN	Benign	0.86
PhyloP100		-0.74

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs36221483;

hg19: chr21-46410070;