21-24900757-A-G

Variant names:

• chr21-24900757-A-G
• rs2829454
• ENST00000441009.1:n.330+55828A>G

Variant summary

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

The ENST00000441009.1(LINC01692):​n.330+55828A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.23 in 152,054 control chromosomes in the GnomAD database, including 5,080 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 0.23 (5080 hom., cov: 32)
• Consequence: LINC01692 ENST00000441009.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.13
• Publications: 5 publications found

Genes affected

LINC01692 (HGNC:52480): (long intergenic non-protein coding RNA 1692)

ENSG00000227090 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.495 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01692	NR_046198.3	n.330+55828A>G		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01692	ENST00000441009.1	n.330+55828A>G		intron_variant	Intron 2 of 3	1
ENSG00000227090	ENST00000446404.1	n.79+1921T>C		intron_variant	Intron 1 of 1	3
LINC01692	ENST00000762004.1	n.285+55852A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.230 AC: 34898 AN: 151934 Hom.: 5069 Cov.: 32

Gnomad AFR AF: 0.0775

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.512

Gnomad SAS AF: 0.338

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.259

Gnomad OTH AF: 0.251

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

GnomAD4 genome AF: 0.230 AC: 34925 AN: 152054 Hom.: 5080 Cov.: 32 AF XY: 0.233 AC XY: 17330 AN XY: 74326

African (AFR) AF: 0.0773 AC: 3209 AN: 41516

American (AMR) AF: 0.386 AC: 5887 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.223 AC: 773 AN: 3472

East Asian (EAS) AF: 0.512 AC: 2645 AN: 5170

South Asian (SAS) AF: 0.340 AC: 1639 AN: 4822

European-Finnish (FIN) AF: 0.225 AC: 2375 AN: 10568

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.259 AC: 17626 AN: 67948

Other (OTH) AF: 0.258 AC: 544 AN: 2110

Alfa AF: 0.247 Hom.: 1744

Bravo AF: 0.239

Asia WGS AF: 0.425 AC: 1479 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	8.1
DANN	Benign	0.83
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs2829454; hg19: chr21-26273071;