rs9825291

Variant names:

• chr3-152787516-C-T
• rs9825291
• XR_007096134.1:n.*99C>T

Variant summary

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

The XR_007096134.1(LOC124909449):​n.*99C>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.582 in 152,044 control chromosomes in the GnomAD database, including 27,427 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 0.58 (27427 hom., cov: 32)
• Consequence: LOC124909449 XR_007096134.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.05
• Publications: 5 publications found

Genes affected

LOC124909449 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.725 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.582 AC: 88446 AN: 151928 Hom.: 27417 Cov.: 32

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.642

Gnomad AMR AF: 0.684

Gnomad ASJ AF: 0.666

Gnomad EAS AF: 0.744

Gnomad SAS AF: 0.730

Gnomad FIN AF: 0.637

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.667

Gnomad OTH AF: 0.595

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

GnomAD4 genome AF: 0.582 AC: 88473 AN: 152044 Hom.: 27427 Cov.: 32 AF XY: 0.585 AC XY: 43512 AN XY: 74328

African (AFR) AF: 0.344 AC: 14250 AN: 41456

American (AMR) AF: 0.684 AC: 10453 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.666 AC: 2311 AN: 3472

East Asian (EAS) AF: 0.744 AC: 3849 AN: 5172

South Asian (SAS) AF: 0.730 AC: 3518 AN: 4822

European-Finnish (FIN) AF: 0.637 AC: 6723 AN: 10550

Middle Eastern (MID) AF: 0.619 AC: 182 AN: 294

European-Non Finnish (NFE) AF: 0.667 AC: 45346 AN: 67982

Other (OTH) AF: 0.595 AC: 1257 AN: 2112

Alfa AF: 0.637 Hom.: 97666

Bravo AF: 0.570

Asia WGS AF: 0.721 AC: 2510 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.4
DANN	Benign	0.64
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs9825291; hg19: chr3-152505305;