rs2321489

Variant names:

• chr8-25725149-C-G
• rs2321489
• XR_001745849.2:n.238+94780C>G

Your query was ambiguous. Multiple possible variants found:

• chr8-25725149-C-G
• chr8-25725149-C-T

Variant summary

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

The XR_001745849.2(LOC107986933):​n.238+94780C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.607 in 151,978 control chromosomes in the GnomAD database, including 28,815 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 0.61 (28815 hom., cov: 33)
• Consequence: LOC107986933 XR_001745849.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.587
• Publications: 2 publications found

Genes affected

LOC107986933 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.69 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.607 AC: 92207 AN: 151858 Hom.: 28795 Cov.: 33

Gnomad AFR AF: 0.464

Gnomad AMI AF: 0.596

Gnomad AMR AF: 0.699

Gnomad ASJ AF: 0.626

Gnomad EAS AF: 0.709

Gnomad SAS AF: 0.550

Gnomad FIN AF: 0.673

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.659

Gnomad OTH AF: 0.624

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

GnomAD4 genome AF: 0.607 AC: 92266 AN: 151978 Hom.: 28815 Cov.: 33 AF XY: 0.609 AC XY: 45219 AN XY: 74274

African (AFR) AF: 0.464 AC: 19218 AN: 41446

American (AMR) AF: 0.700 AC: 10674 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.626 AC: 2170 AN: 3466

East Asian (EAS) AF: 0.710 AC: 3652 AN: 5146

South Asian (SAS) AF: 0.549 AC: 2648 AN: 4820

European-Finnish (FIN) AF: 0.673 AC: 7118 AN: 10572

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.659 AC: 44775 AN: 67966

Other (OTH) AF: 0.627 AC: 1323 AN: 2110

Alfa AF: 0.635 Hom.: 3905

Bravo AF: 0.602

Asia WGS AF: 0.651 AC: 2259 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.95
DANN	Benign	0.49
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs2321489; hg19: chr8-25582665;