rs36221776

Variant names:

• chr21-44993811-C-A
• rs36221776
• ENST00000434081.1:n.183+93G>T

Variant summary

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

The ENST00000434081.1(LINC00163):​n.183+93G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 147,684 control chromosomes in the GnomAD database, including 2,624 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 0.19 (2592 hom., cov: 32)
  • Exomes 𝑓: 0.060 (32 hom.)
• Consequence: LINC00163 ENST00000434081.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.239 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00163	NR_033840.1		n.183+93G>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00163	ENST00000434081.1	TSL:1	n.183+93G>T		intron	N/A
	LINC00163	ENST00000439088.1	TSL:1	n.166+93G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.189 AC: 27222 AN: 143968 Hom.: 2592 Cov.: 32

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.245

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.132

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.181

GnomAD4 exome AF: 0.0601 AC: 218 AN: 3626 Hom.: 32 AF XY: 0.0649 AC XY: 151 AN XY: 2326

African (AFR) AF: 0.0313 AC: 1 AN: 32

American (AMR) AF: 0.125 AC: 2 AN: 16

Ashkenazi Jewish (ASJ) AF: 0.0625 AC: 3 AN: 48

East Asian (EAS) AF: 0.0278 AC: 1 AN: 36

South Asian (SAS) AF: 0.0236 AC: 23 AN: 974

European-Finnish (FIN) AF: 0.00917 AC: 2 AN: 218

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 16

European-Non Finnish (NFE) AF: 0.0832 AC: 175 AN: 2104

Other (OTH) AF: 0.0604 AC: 11 AN: 182

GnomAD4 genome AF: 0.189 AC: 27229 AN: 144058 Hom.: 2592 Cov.: 32 AF XY: 0.188 AC XY: 13307 AN XY: 70710

African (AFR) AF: 0.152 AC: 5207 AN: 34312

American (AMR) AF: 0.245 AC: 3665 AN: 14942

Ashkenazi Jewish (ASJ) AF: 0.239 AC: 828 AN: 3458

East Asian (EAS) AF: 0.169 AC: 864 AN: 5118

South Asian (SAS) AF: 0.116 AC: 555 AN: 4794

European-Finnish (FIN) AF: 0.178 AC: 1869 AN: 10508

Middle Eastern (MID) AF: 0.122 AC: 35 AN: 288

European-Non Finnish (NFE) AF: 0.202 AC: 13652 AN: 67704

Other (OTH) AF: 0.184 AC: 373 AN: 2030

Alfa AF: 0.193 Hom.: 858

Bravo AF: 0.187

Asia WGS AF: 0.158 AC: 548 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.57
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs36221776; hg19: chr21-46413726;