9-125241509-GCC-GCCC

Position:

• chr9-125241509-GCC-GCCC

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.0072 (10 hom., cov: 0)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.122

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BS2: High Homozygotes in GnomAd4 at 10 gene

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: 0.00723 AC: 1098 AN: 151884 Hom.: 10 Cov.: 0

Gnomad AFR AF: 0.00246

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.00354

Gnomad ASJ AF: 0.0132

Gnomad EAS AF: 0.000194

Gnomad SAS AF: 0.00124

Gnomad FIN AF: 0.00521

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0122

Gnomad OTH AF: 0.00144

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

GnomAD4 genome AF: 0.00722 AC: 1097 AN: 152002 Hom.: 10 Cov.: 0 AF XY: 0.00665 AC XY: 494 AN XY: 74284

Gnomad4 AFR AF: 0.00246

Gnomad4 AMR AF: 0.00354

Gnomad4 ASJ AF: 0.0132

Gnomad4 EAS AF: 0.000194

Gnomad4 SAS AF: 0.00124

Gnomad4 FIN AF: 0.00521

Gnomad4 NFE AF: 0.0122

Gnomad4 OTH AF: 0.00143

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3216733; hg19: chr9-128003788;