chr9-92119797-G-A

Position:

• chr9-92119797-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 0.531 in 152,066 control chromosomes in the GnomAD database, including 23,985 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 0.53 (23985 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0480

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.802 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: 0.531 AC: 80673 AN: 151948 Hom.: 23936 Cov.: 33

Gnomad AFR AF: 0.809

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.553

Gnomad ASJ AF: 0.512

Gnomad EAS AF: 0.427

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.439

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.477

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

GnomAD4 genome AF: 0.531 AC: 80787 AN: 152066 Hom.: 23985 Cov.: 33 AF XY: 0.534 AC XY: 39676 AN XY: 74308

Gnomad4 AFR AF: 0.810

Gnomad4 AMR AF: 0.553

Gnomad4 ASJ AF: 0.512

Gnomad4 EAS AF: 0.428

Gnomad4 SAS AF: 0.454

Gnomad4 FIN AF: 0.439

Gnomad4 NFE AF: 0.390

Gnomad4 OTH AF: 0.480

Alfa AF: 0.522 Hom.: 3862

Bravo AF: 0.550

Asia WGS AF: 0.481 AC: 1673 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.2
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: rs7023075; hg19: chr9-94882079;