9-85238445-G-A

Position:

• chr9-85238445-G-A

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 0.695 in 151,994 control chromosomes in the GnomAD database, including 38,645 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 0.70 (38645 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.724

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.908 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: 0.695 AC: 105571 AN: 151876 Hom.: 38578 Cov.: 32

Gnomad AFR AF: 0.916

Gnomad AMI AF: 0.349

Gnomad AMR AF: 0.683

Gnomad ASJ AF: 0.621

Gnomad EAS AF: 0.882

Gnomad SAS AF: 0.707

Gnomad FIN AF: 0.643

Gnomad MID AF: 0.694

Gnomad NFE AF: 0.565

Gnomad OTH AF: 0.699

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

GnomAD4 genome AF: 0.695 AC: 105697 AN: 151994 Hom.: 38645 Cov.: 32 AF XY: 0.699 AC XY: 51954 AN XY: 74288

Gnomad4 AFR AF: 0.916

Gnomad4 AMR AF: 0.683

Gnomad4 ASJ AF: 0.621

Gnomad4 EAS AF: 0.882

Gnomad4 SAS AF: 0.707

Gnomad4 FIN AF: 0.643

Gnomad4 NFE AF: 0.565

Gnomad4 OTH AF: 0.703

Alfa AF: 0.593 Hom.: 11412

Bravo AF: 0.711

Asia WGS AF: 0.799 AC: 2770 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.6
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7040848; hg19: chr9-87853360;