9-5188078-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 0.588 in 152,146 control chromosomes in the GnomAD database, including 28,149 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 0.59 (28149 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.792

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.816 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: 0.588 AC: 89384 AN: 152028 Hom.: 28102 Cov.: 33

Gnomad AFR AF: 0.823

Gnomad AMI AF: 0.600

Gnomad AMR AF: 0.561

Gnomad ASJ AF: 0.550

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.498

Gnomad FIN AF: 0.547

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.482

Gnomad OTH AF: 0.580

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

GnomAD4 genome AF: 0.588 AC: 89487 AN: 152146 Hom.: 28149 Cov.: 33 AF XY: 0.586 AC XY: 43589 AN XY: 74374

Gnomad4 AFR AF: 0.823

Gnomad4 AMR AF: 0.561

Gnomad4 ASJ AF: 0.550

Gnomad4 EAS AF: 0.380

Gnomad4 SAS AF: 0.499

Gnomad4 FIN AF: 0.547

Gnomad4 NFE AF: 0.482

Gnomad4 OTH AF: 0.582

Alfa AF: 0.500 Hom.: 24837

Bravo AF: 0.598

Asia WGS AF: 0.497 AC: 1726 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.2
Dann	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10758677; hg19: chr9-5188078;