rs9380350

chr6-33159088-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 0.143 in 140,746 control chromosomes in the GnomAD database, including 3,174 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 0.14 (3174 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.371

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.382 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: 0.143 AC: 20070 AN: 140636 Hom.: 3162 Cov.: 31

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.0680

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.0523

Gnomad EAS AF: 0.396

Gnomad SAS AF: 0.0702

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.143 AC: 20100 AN: 140746 Hom.: 3174 Cov.: 31 AF XY: 0.146 AC XY: 10029 AN XY: 68716

Gnomad4 AFR AF: 0.121

Gnomad4 AMR AF: 0.241

Gnomad4 ASJ AF: 0.0523

Gnomad4 EAS AF: 0.398

Gnomad4 SAS AF: 0.0714

Gnomad4 FIN AF: 0.173

Gnomad4 NFE AF: 0.125

Gnomad4 OTH AF: 0.149

Alfa AF: 0.174 Hom.: 409

Bravo AF: 0.205

Asia WGS AF: 0.216 AC: 738 AN: 3428

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	5.3
Dann	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9380350; hg19: chr6-33126865;