chr9-75455766-G-C

Position:

• chr9-75455766-G-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 0.498 in 152,084 control chromosomes in the GnomAD database, including 19,437 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 0.50 (19437 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.415

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 (AMR) allele frequency at 95% confidence interval = 0.543 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: 0.498 AC: 75658 AN: 151966 Hom.: 19426 Cov.: 33

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.409

Gnomad AMR AF: 0.553

Gnomad ASJ AF: 0.434

Gnomad EAS AF: 0.313

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.657

Gnomad MID AF: 0.436

Gnomad NFE AF: 0.535

Gnomad OTH AF: 0.506

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

GnomAD4 genome AF: 0.498 AC: 75705 AN: 152084 Hom.: 19437 Cov.: 33 AF XY: 0.499 AC XY: 37119 AN XY: 74324

Gnomad4 AFR AF: 0.429

Gnomad4 AMR AF: 0.553

Gnomad4 ASJ AF: 0.434

Gnomad4 EAS AF: 0.312

Gnomad4 SAS AF: 0.312

Gnomad4 FIN AF: 0.657

Gnomad4 NFE AF: 0.535

Gnomad4 OTH AF: 0.502

Alfa AF: 0.522 Hom.: 2612

Bravo AF: 0.490

Asia WGS AF: 0.287 AC: 995 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	5.6
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2026406; hg19: chr9-78070682;