rs9277916

chr6-33157659-C-Gchr6-33157659-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 0.311 in 152,106 control chromosomes in the GnomAD database, including 7,852 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 0.31 (7852 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.539 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: 0.311 AC: 47248 AN: 151988 Hom.: 7855 Cov.: 32

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.453

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.498

Gnomad EAS AF: 0.360

Gnomad SAS AF: 0.557

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.331

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.311 AC: 47253 AN: 152106 Hom.: 7852 Cov.: 32 AF XY: 0.313 AC XY: 23308 AN XY: 74348

Gnomad4 AFR AF: 0.233

Gnomad4 AMR AF: 0.310

Gnomad4 ASJ AF: 0.498

Gnomad4 EAS AF: 0.360

Gnomad4 SAS AF: 0.556

Gnomad4 FIN AF: 0.261

Gnomad4 NFE AF: 0.331

Gnomad4 OTH AF: 0.342

Alfa AF: 0.183 Hom.: 401

Bravo AF: 0.308

Asia WGS AF: 0.432 AC: 1500 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.56
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9277916; hg19: chr6-33125436;