21-44990442-G-T

Variant names:

• chr21-44990442-G-T
• rs36221774
• ENST00000434081.1:n.1577C>A

Variant summary

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

The ENST00000434081.1(LINC00163):​n.1577C>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 0.18 in 152,360 control chromosomes in the GnomAD database, including 2,627 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 0.18 (2625 hom., cov: 33)
  • Exomes 𝑓: 0.18 (2 hom.)
• Consequence: LINC00163 ENST00000434081.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365
• Publications: 1 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.236 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.1577C>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.1577C>A		non_coding_transcript_exon	Exon 2 of 2
	LINC00163	ENST00000439088.1	TSL:1	n.1557C>A		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.180 AC: 27404 AN: 152052 Hom.: 2627 Cov.: 33

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.179

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.176

GnomAD4 exome AF: 0.181 AC: 34 AN: 188 Hom.: 2 Cov.: 0 AF XY: 0.184 AC XY: 29 AN XY: 158

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 6

South Asian (SAS) AC: 0 AN: 0

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

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.198 AC: 32 AN: 162

Other (OTH) AF: 0.00 AC: 0 AN: 12

GnomAD4 genome AF: 0.180 AC: 27409 AN: 152172 Hom.: 2625 Cov.: 33 AF XY: 0.181 AC XY: 13457 AN XY: 74404

African (AFR) AF: 0.133 AC: 5532 AN: 41514

American (AMR) AF: 0.243 AC: 3715 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.239 AC: 830 AN: 3470

East Asian (EAS) AF: 0.169 AC: 872 AN: 5156

South Asian (SAS) AF: 0.119 AC: 576 AN: 4822

European-Finnish (FIN) AF: 0.179 AC: 1898 AN: 10616

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.197 AC: 13387 AN: 67980

Other (OTH) AF: 0.179 AC: 378 AN: 2114

Alfa AF: 0.0900 Hom.: 118

Bravo AF: 0.186

Asia WGS AF: 0.158 AC: 550 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.3
DANN	Benign	0.59
PhyloP100		0.36

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: rs36221774;

hg19: chr21-46410357;