9-16129632-A-G

Variant names:

• chr9-16129632-A-G
• rs1536689

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 0.299 in 152,208 control chromosomes in the GnomAD database, including 7,799 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 0.30 (7799 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.464 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45444 AN: 152088 Hom.: 7755 Cov.: 33

Gnomad AFR AF: 0.469

Gnomad AMI AF: 0.443

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.311

Gnomad EAS AF: 0.235

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.170

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.226

Gnomad OTH AF: 0.280

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

GnomAD4 genome AF: 0.299 AC: 45555 AN: 152208 Hom.: 7799 Cov.: 33 AF XY: 0.297 AC XY: 22119 AN XY: 74420

Gnomad4 AFR AF: 0.470

Gnomad4 AMR AF: 0.247

Gnomad4 ASJ AF: 0.311

Gnomad4 EAS AF: 0.235

Gnomad4 SAS AF: 0.361

Gnomad4 FIN AF: 0.170

Gnomad4 NFE AF: 0.226

Gnomad4 OTH AF: 0.277

Alfa AF: 0.244 Hom.: 4445

Bravo AF: 0.308

Asia WGS AF: 0.316 AC: 1103 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.27
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1536689; hg19: chr9-16129630;