9-5200060-A-G

Position:

• chr9-5200060-A-G

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 0.3 in 152,070 control chromosomes in the GnomAD database, including 6,973 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 0.30 (6973 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0710

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.337 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: 0.300 AC: 45626 AN: 151952 Hom.: 6965 Cov.: 32

Gnomad AFR AF: 0.342

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.351

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.293

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

GnomAD4 genome AF: 0.300 AC: 45677 AN: 152070 Hom.: 6973 Cov.: 32 AF XY: 0.305 AC XY: 22644 AN XY: 74312

Gnomad4 AFR AF: 0.342

Gnomad4 AMR AF: 0.284

Gnomad4 ASJ AF: 0.251

Gnomad4 EAS AF: 0.256

Gnomad4 SAS AF: 0.339

Gnomad4 FIN AF: 0.351

Gnomad4 NFE AF: 0.275

Gnomad4 OTH AF: 0.294

Alfa AF: 0.288 Hom.: 2959

Bravo AF: 0.292

Asia WGS AF: 0.313 AC: 1084 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10491651; hg19: chr9-5200060;