chr9-110609401-A-C

Position:

• chr9-110609401-A-C

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 0.159 in 152,180 control chromosomes in the GnomAD database, including 2,012 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 0.16 (2012 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.800

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.169 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: 0.159 AC: 24162 AN: 152062 Hom.: 2010 Cov.: 33

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.0658

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.159 AC: 24182 AN: 152180 Hom.: 2012 Cov.: 33 AF XY: 0.158 AC XY: 11733 AN XY: 74384

Gnomad4 AFR AF: 0.158

Gnomad4 AMR AF: 0.130

Gnomad4 ASJ AF: 0.158

Gnomad4 EAS AF: 0.0659

Gnomad4 SAS AF: 0.133

Gnomad4 FIN AF: 0.181

Gnomad4 NFE AF: 0.171

Gnomad4 OTH AF: 0.161

Alfa AF: 0.165 Hom.: 387

Bravo AF: 0.155

Asia WGS AF: 0.0970 AC: 341 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	8.2
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10817049; hg19: chr9-113371681;