rs302923

Variant names:

• chr9-132697260-T-C
• rs302923

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.157 in 152,116 control chromosomes in the GnomAD database, including 3,841 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 0.16 (3841 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.678

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.406 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: 0.157 AC: 23905 AN: 151998 Hom.: 3835 Cov.: 33

Gnomad AFR AF: 0.411

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.0331

Gnomad EAS AF: 0.117

Gnomad SAS AF: 0.0462

Gnomad FIN AF: 0.0453

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0454

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.157 AC: 23947 AN: 152116 Hom.: 3841 Cov.: 33 AF XY: 0.154 AC XY: 11488 AN XY: 74382

Gnomad4 AFR AF: 0.411

Gnomad4 AMR AF: 0.135

Gnomad4 ASJ AF: 0.0331

Gnomad4 EAS AF: 0.117

Gnomad4 SAS AF: 0.0460

Gnomad4 FIN AF: 0.0453

Gnomad4 NFE AF: 0.0454

Gnomad4 OTH AF: 0.128

Alfa AF: 0.0727 Hom.: 461

Bravo AF: 0.177

Asia WGS AF: 0.0850 AC: 296 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.6
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs302923; hg19: chr9-135572647;