chr9-129734338-C-T

Variant names:

• chr9-129734338-C-T
• rs11999368

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 0.247 in 152,070 control chromosomes in the GnomAD database, including 6,095 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 0.25 (6095 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.797
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 = 0.443 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: 0.247 AC: 37525 AN: 151952 Hom.: 6095 Cov.: 32

Gnomad AFR AF: 0.449

Gnomad AMI AF: 0.372

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.426

Gnomad SAS AF: 0.295

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.247 AC: 37554 AN: 152070 Hom.: 6095 Cov.: 32 AF XY: 0.246 AC XY: 18299 AN XY: 74322

African (AFR) AF: 0.448 AC: 18557 AN: 41414

American (AMR) AF: 0.182 AC: 2790 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.179 AC: 620 AN: 3468

East Asian (EAS) AF: 0.425 AC: 2195 AN: 5168

South Asian (SAS) AF: 0.295 AC: 1421 AN: 4818

European-Finnish (FIN) AF: 0.123 AC: 1299 AN: 10600

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.144 AC: 9800 AN: 67998

Other (OTH) AF: 0.231 AC: 487 AN: 2108

Alfa AF: 0.208 Hom.: 1814

Bravo AF: 0.261

Asia WGS AF: 0.344 AC: 1196 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	5.5
DANN	Benign	0.60
PhyloP100		0.80

Splicing

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

Other links and lift over

dbSNP: rs11999368; hg19: chr9-132496617;