rs11789407

chr9-118597268-C-Achr9-118597268-C-T

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 0.433 in 151,976 control chromosomes in the GnomAD database, including 14,949 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 0.43 (14949 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.309

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.5 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.433 AC: 65682 AN: 151858 Hom.: 14937 Cov.: 32

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.637

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.505

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.504

Gnomad OTH AF: 0.464

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

GnomAD4 genome AF: 0.433 AC: 65736 AN: 151976 Hom.: 14949 Cov.: 32 AF XY: 0.428 AC XY: 31763 AN XY: 74280

Gnomad4 AFR AF: 0.341

Gnomad4 AMR AF: 0.396

Gnomad4 ASJ AF: 0.637

Gnomad4 EAS AF: 0.166

Gnomad4 SAS AF: 0.282

Gnomad4 FIN AF: 0.505

Gnomad4 NFE AF: 0.504

Gnomad4 OTH AF: 0.460

Alfa AF: 0.458 Hom.: 2817

Bravo AF: 0.420

Asia WGS AF: 0.249 AC: 869 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	4.7
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11789407; hg19: chr9-121359546;