chr9-16901069-C-A

Position:

• chr9-16901069-C-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 0.546 in 149,652 control chromosomes in the GnomAD database, including 23,228 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 0.55 (23228 hom., cov: 24)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.407

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 (NFE) allele frequency at 95% confidence interval = 0.62 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: 0.546 AC: 81624 AN: 149542 Hom.: 23219 Cov.: 24

Gnomad AFR AF: 0.505

Gnomad AMI AF: 0.597

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.327

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.597

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.625

Gnomad OTH AF: 0.553

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

GnomAD4 genome AF: 0.546 AC: 81648 AN: 149652 Hom.: 23228 Cov.: 24 AF XY: 0.536 AC XY: 39123 AN XY: 72956

Gnomad4 AFR AF: 0.505

Gnomad4 AMR AF: 0.435

Gnomad4 ASJ AF: 0.529

Gnomad4 EAS AF: 0.327

Gnomad4 SAS AF: 0.230

Gnomad4 FIN AF: 0.597

Gnomad4 NFE AF: 0.625

Gnomad4 OTH AF: 0.547

Alfa AF: 0.558 Hom.: 2702

Bravo AF: 0.541

Asia WGS AF: 0.288 AC: 1005 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.2
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs62543565; hg19: chr9-16901067;