21-44989850-A-G

Variant names:

• chr21-44989850-A-G
• rs4819004
• ENST00000434081.1:n.*14T>C

Variant summary

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

The ENST00000434081.1(LINC00163):​n.*14T>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 152,228 control chromosomes in the GnomAD database, including 40,454 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 (40451 hom., cov: 34)
  • Exomes 𝑓: 1.0 (3 hom.)
• Consequence: LINC00163 ENST00000434081.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.65
• Publications: 4 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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.809 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.*14T>C		downstream_gene	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00163	ENST00000434081.1	TSL:1	n.*14T>C		downstream_gene	N/A
	LINC00163	ENST00000439088.1	TSL:1	n.*14T>C		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.721 AC: 109626 AN: 152104 Hom.: 40443 Cov.: 34

Gnomad AFR AF: 0.555

Gnomad AMI AF: 0.750

Gnomad AMR AF: 0.779

Gnomad ASJ AF: 0.769

Gnomad EAS AF: 0.831

Gnomad SAS AF: 0.823

Gnomad FIN AF: 0.790

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.779

Gnomad OTH AF: 0.732

GnomAD4 exome AF: 1.00 AC: 6 AN: 6 Hom.: 3 Cov.: 0 AF XY: 1.00 AC XY: 2 AN XY: 2

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) AF: 1.00 AC: 2 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 1.00 AC: 4 AN: 4

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.720 AC: 109668 AN: 152222 Hom.: 40451 Cov.: 34 AF XY: 0.724 AC XY: 53906 AN XY: 74438

African (AFR) AF: 0.554 AC: 23005 AN: 41516

American (AMR) AF: 0.779 AC: 11919 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.769 AC: 2671 AN: 3472

East Asian (EAS) AF: 0.830 AC: 4304 AN: 5186

South Asian (SAS) AF: 0.824 AC: 3979 AN: 4828

European-Finnish (FIN) AF: 0.790 AC: 8373 AN: 10594

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

European-Non Finnish (NFE) AF: 0.779 AC: 52965 AN: 68008

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

Alfa AF: 0.753 Hom.: 7378

Bravo AF: 0.710

Asia WGS AF: 0.815 AC: 2831 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.0
DANN	Benign	0.26
PhyloP100		-1.6
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs4819004; hg19: chr21-46409765;