rs9380351

chr6-33161969-G-Achr6-33161969-G-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 0.191 in 152,266 control chromosomes in the GnomAD database, including 3,310 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 0.19 (3310 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.803

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.463 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: 0.191 AC: 29081 AN: 152148 Hom.: 3296 Cov.: 33

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.477

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.191 AC: 29120 AN: 152266 Hom.: 3310 Cov.: 33 AF XY: 0.196 AC XY: 14568 AN XY: 74454

Gnomad4 AFR AF: 0.151

Gnomad4 AMR AF: 0.302

Gnomad4 ASJ AF: 0.103

Gnomad4 EAS AF: 0.478

Gnomad4 SAS AF: 0.166

Gnomad4 FIN AF: 0.225

Gnomad4 NFE AF: 0.171

Gnomad4 OTH AF: 0.201

Alfa AF: 0.184 Hom.: 4523

Bravo AF: 0.201

Asia WGS AF: 0.266 AC: 923 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
Cadd	Benign	11
Dann	Benign	0.92

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9380351; hg19: chr6-33129746;