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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.112

Gnomad4 AMR AF: 0.150

Gnomad4 ASJ AF: 0.139

Gnomad4 EAS AF: 0.384

Gnomad4 SAS AF: 0.244

Gnomad4 FIN AF: 0.190

Gnomad4 NFE AF: 0.149

Gnomad4 OTH AF: 0.166

Alfa AF: 0.143 Hom.: 2106

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13285273; hg19: chr9-103691860;