rs4819004

Positions:

• chr21-44989850-A-G
• chr21-44989850-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The 21-44989850-A-G 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 NR_033840.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.65

Genes affected

LINC00163 (HGNC:33165): (long intergenic non-protein coding RNA 163)

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00163	NR_033840.1			downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00163	ENST00000434081.1			downstream_gene_variant		1
LINC00163	ENST00000439088.1			downstream_gene_variant		1

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

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 1.00

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

Gnomad4 AFR AF: 0.554

Gnomad4 AMR AF: 0.779

Gnomad4 ASJ AF: 0.769

Gnomad4 EAS AF: 0.830

Gnomad4 SAS AF: 0.824

Gnomad4 FIN AF: 0.790

Gnomad4 NFE AF: 0.779

Gnomad4 OTH AF: 0.734

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.0
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4819004; hg19: chr21-46409765;