rs9982023

Variant names:

• chr21-28542904-A-G
• rs9982023
• ENST00000825125.1:n.492A>G

Variant summary

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

The ENST00000825125.1(LINC00161):​n.492A>G 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 0.123 in 152,066 control chromosomes in the GnomAD database, including 2,004 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 0.12 (2004 hom., cov: 31)
• Consequence: LINC00161 ENST00000825125.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.245
• Publications: 4 publications found

Genes affected

LINC00161 (HGNC:17138): (long intergenic non-protein coding RNA 161)

ENSG00000232855 (HGNC:58104):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.284 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00161	ENST00000825125.1	n.492A>G		non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000232855	ENST00000430247.1	n.126+34371T>C		intron_variant	Intron 2 of 4	5
ENSG00000232855	ENST00000433310.6	n.456+34315T>C		intron_variant	Intron 3 of 4	2

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18661 AN: 151946 Hom.: 2001 Cov.: 31

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.0879

Gnomad AMR AF: 0.0603

Gnomad ASJ AF: 0.0712

Gnomad EAS AF: 0.0129

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.0428

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0620

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.123 AC: 18686 AN: 152066 Hom.: 2004 Cov.: 31 AF XY: 0.120 AC XY: 8895 AN XY: 74362

African (AFR) AF: 0.289 AC: 11962 AN: 41432

American (AMR) AF: 0.0601 AC: 918 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0712 AC: 247 AN: 3470

East Asian (EAS) AF: 0.0132 AC: 68 AN: 5168

South Asian (SAS) AF: 0.102 AC: 492 AN: 4820

European-Finnish (FIN) AF: 0.0428 AC: 454 AN: 10604

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0620 AC: 4217 AN: 68008

Other (OTH) AF: 0.104 AC: 219 AN: 2108

Alfa AF: 0.110 Hom.: 259

Bravo AF: 0.131

Asia WGS AF: 0.0890 AC: 311 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.1
DANN	Benign	0.47
PhyloP100		-0.24
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: rs9982023; hg19: chr21-29915226;