rs302923

Positions:

• chr9-132697260-T-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;