9-32625624-C-T

Position:

• chr9-32625624-C-T

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 0.0884 in 152,090 control chromosomes in the GnomAD database, including 656 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 0.088 (656 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.267

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.128 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0884 AC: 13441 AN: 151972 Hom.: 659 Cov.: 32

Gnomad AFR AF: 0.0695

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.0608

Gnomad ASJ AF: 0.0963

Gnomad EAS AF: 0.0874

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.0990

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.0773

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

GnomAD4 genome AF: 0.0884 AC: 13443 AN: 152090 Hom.: 656 Cov.: 32 AF XY: 0.0884 AC XY: 6575 AN XY: 74338

Gnomad4 AFR AF: 0.0695

Gnomad4 AMR AF: 0.0607

Gnomad4 ASJ AF: 0.0963

Gnomad4 EAS AF: 0.0870

Gnomad4 SAS AF: 0.137

Gnomad4 FIN AF: 0.0990

Gnomad4 NFE AF: 0.102

Gnomad4 OTH AF: 0.0788

Alfa AF: 0.0955 Hom.: 968

Bravo AF: 0.0824

Asia WGS AF: 0.132 AC: 459 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.1
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10813843; hg19: chr9-32625622; COSMIC: COSV54265372;