chr9-111865238-A-G

Position:

• chr9-111865238-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 0.103 in 152,048 control chromosomes in the GnomAD database, including 1,093 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 0.10 (1093 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.208

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.189 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: 0.103 AC: 15599 AN: 151930 Hom.: 1087 Cov.: 31

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.210

Gnomad AMR AF: 0.0527

Gnomad ASJ AF: 0.0524

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.0621

Gnomad FIN AF: 0.0553

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0682

Gnomad OTH AF: 0.0863

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

GnomAD4 genome AF: 0.103 AC: 15614 AN: 152048 Hom.: 1093 Cov.: 31 AF XY: 0.0999 AC XY: 7426 AN XY: 74304

Gnomad4 AFR AF: 0.193

Gnomad4 AMR AF: 0.0526

Gnomad4 ASJ AF: 0.0524

Gnomad4 EAS AF: 0.141

Gnomad4 SAS AF: 0.0619

Gnomad4 FIN AF: 0.0553

Gnomad4 NFE AF: 0.0682

Gnomad4 OTH AF: 0.0854

Alfa AF: 0.0947 Hom.: 155

Bravo AF: 0.108

Asia WGS AF: 0.0880 AC: 307 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	1.6
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7863596; hg19: chr9-114627518;