9-135328856-C-G

Variant names:

• chr9-135328856-C-G
• rs9410016

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.34 in 152,114 control chromosomes in the GnomAD database, including 9,965 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 0.34 (9965 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0390
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.474 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: 0.340 AC: 51644 AN: 151996 Hom.: 9953 Cov.: 33

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.470

Gnomad SAS AF: 0.490

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.324

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

GnomAD4 genome AF: 0.340 AC: 51672 AN: 152114 Hom.: 9965 Cov.: 33 AF XY: 0.348 AC XY: 25898 AN XY: 74364

African (AFR) AF: 0.160 AC: 6651 AN: 41530

American (AMR) AF: 0.298 AC: 4554 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.352 AC: 1222 AN: 3468

East Asian (EAS) AF: 0.469 AC: 2418 AN: 5154

South Asian (SAS) AF: 0.491 AC: 2368 AN: 4826

European-Finnish (FIN) AF: 0.535 AC: 5663 AN: 10584

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.408 AC: 27734 AN: 67948

Other (OTH) AF: 0.330 AC: 697 AN: 2114

Alfa AF: 0.388 Hom.: 1558

Bravo AF: 0.312

Asia WGS AF: 0.459 AC: 1593 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	1.4
DANN	Benign	0.60
PhyloP100		-0.039

Splicing

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

Other links and lift over

dbSNP: rs9410016; hg19: chr9-138220702;