rs13285273

Variant names:

• chr9-100929578-G-A
• rs13285273

Your query was ambiguous. Multiple possible variants found:

• chr9-100929578-G-A
• chr9-100929578-G-T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.152 in 152,122 control chromosomes in the GnomAD database, including 2,054 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 0.15 (2054 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.29).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.37 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.152 AC: 23178 AN: 152004 Hom.: 2053 Cov.: 32

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.0691

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.384

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.152 AC: 23192 AN: 152122 Hom.: 2054 Cov.: 32 AF XY: 0.158 AC XY: 11732 AN XY: 74374

African (AFR) AF: 0.112 AC: 4654 AN: 41498

American (AMR) AF: 0.150 AC: 2294 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.139 AC: 483 AN: 3470

East Asian (EAS) AF: 0.384 AC: 1980 AN: 5160

South Asian (SAS) AF: 0.244 AC: 1175 AN: 4820

European-Finnish (FIN) AF: 0.190 AC: 2011 AN: 10588

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.149 AC: 10126 AN: 67998

Other (OTH) AF: 0.166 AC: 351 AN: 2112

Alfa AF: 0.143 Hom.: 2490

Bravo AF: 0.147

Asia WGS AF: 0.306 AC: 1064 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.29
CADD	Benign	13
DANN	Benign	0.77
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs13285273; hg19: chr9-103691860;