rs2226351

Variant names:

• chr21-24965625-A-G
• rs2226351
• ENST00000441009.1:n.331-64159A>G

Your query was ambiguous. Multiple possible variants found:

• chr21-24965625-A-G
• chr21-24965625-A-T

Variant summary

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

The ENST00000441009.1(LINC01692):​n.331-64159A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.729 in 152,070 control chromosomes in the GnomAD database, including 43,680 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 0.73 (43680 hom., cov: 32)
• Consequence: LINC01692 ENST00000441009.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.320
• Publications: 3 publications found

Genes affected

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

ENSG00000230379 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.919 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000441009.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01692	NR_046198.3		n.331-64159A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01692	ENST00000441009.1	TSL:1	n.331-64159A>G		intron	N/A
	ENSG00000230379	ENST00000444178.1	TSL:3	n.116-27001T>C		intron	N/A
	LINC01692	ENST00000762004.1		n.286-64159A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.729 AC: 110790 AN: 151952 Hom.: 43662 Cov.: 32

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.746

Gnomad AMR AF: 0.832

Gnomad ASJ AF: 0.756

Gnomad EAS AF: 0.941

Gnomad SAS AF: 0.785

Gnomad FIN AF: 0.866

Gnomad MID AF: 0.842

Gnomad NFE AF: 0.864

Gnomad OTH AF: 0.761

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

GnomAD4 genome AF: 0.729 AC: 110843 AN: 152070 Hom.: 43680 Cov.: 32 AF XY: 0.731 AC XY: 54336 AN XY: 74330

African (AFR) AF: 0.397 AC: 16471 AN: 41474

American (AMR) AF: 0.832 AC: 12683 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.756 AC: 2625 AN: 3470

East Asian (EAS) AF: 0.941 AC: 4867 AN: 5172

South Asian (SAS) AF: 0.785 AC: 3787 AN: 4824

European-Finnish (FIN) AF: 0.866 AC: 9168 AN: 10590

Middle Eastern (MID) AF: 0.840 AC: 247 AN: 294

European-Non Finnish (NFE) AF: 0.864 AC: 58706 AN: 67974

Other (OTH) AF: 0.761 AC: 1609 AN: 2114

Alfa AF: 0.788 Hom.: 6156

Bravo AF: 0.716

Asia WGS AF: 0.814 AC: 2831 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.8
DANN	Benign	0.66
PhyloP100		0.32

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2226351;

hg19: chr21-26337939;