21-44989634-A-G

Variant names:

• chr21-44989634-A-G
• rs11088976
• ENST00000434081.1:n.*230T>C

Variant summary

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

The ENST00000434081.1(LINC00163):​n.*230T>C variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.72 in 152,142 control chromosomes in the GnomAD database, including 40,369 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 0.72 (40369 hom., cov: 34)
• Consequence: LINC00163 ENST00000434081.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.38
• 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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.809 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00163	NR_033840.1	n.*230T>C		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00163	ENST00000434081.1	n.*230T>C		downstream_gene_variant		1
LINC00163	ENST00000439088.1	n.*230T>C		downstream_gene_variant		1

Frequencies

GnomAD3 genomes AF: 0.720 AC: 109479 AN: 152024 Hom.: 40361 Cov.: 34

Gnomad AFR AF: 0.554

Gnomad AMI AF: 0.749

Gnomad AMR AF: 0.779

Gnomad ASJ AF: 0.769

Gnomad EAS AF: 0.830

Gnomad SAS AF: 0.820

Gnomad FIN AF: 0.789

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.779

Gnomad OTH AF: 0.732

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.720 AC: 109521 AN: 152142 Hom.: 40369 Cov.: 34 AF XY: 0.723 AC XY: 53810 AN XY: 74384

African (AFR) AF: 0.553 AC: 22942 AN: 41472

American (AMR) AF: 0.779 AC: 11915 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.769 AC: 2669 AN: 3470

East Asian (EAS) AF: 0.830 AC: 4291 AN: 5172

South Asian (SAS) AF: 0.821 AC: 3958 AN: 4822

European-Finnish (FIN) AF: 0.789 AC: 8364 AN: 10598

Middle Eastern (MID) AF: 0.741 AC: 218 AN: 294

European-Non Finnish (NFE) AF: 0.778 AC: 52932 AN: 67994

Other (OTH) AF: 0.734 AC: 1550 AN: 2112

Alfa AF: 0.706 Hom.: 2540

Bravo AF: 0.709

Asia WGS AF: 0.814 AC: 2827 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.74
DANN	Benign	0.28
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs11088976; hg19: chr21-46409549;