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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124909449	XR_007096134.1	n.*99C>T		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;