rs9368570

chr6-28708416-G-A

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 0.293 in 151,826 control chromosomes in the GnomAD database, including 6,901 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 0.29 (6901 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.855

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.511 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: 0.293 AC: 44472 AN: 151708 Hom.: 6898 Cov.: 31

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.465

Gnomad AMR AF: 0.374

Gnomad ASJ AF: 0.316

Gnomad EAS AF: 0.527

Gnomad SAS AF: 0.342

Gnomad FIN AF: 0.267

Gnomad MID AF: 0.287

Gnomad NFE AF: 0.263

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.293 AC: 44490 AN: 151826 Hom.: 6901 Cov.: 31 AF XY: 0.298 AC XY: 22131 AN XY: 74194

Gnomad4 AFR AF: 0.278

Gnomad4 AMR AF: 0.374

Gnomad4 ASJ AF: 0.316

Gnomad4 EAS AF: 0.527

Gnomad4 SAS AF: 0.343

Gnomad4 FIN AF: 0.267

Gnomad4 NFE AF: 0.263

Gnomad4 OTH AF: 0.310

Alfa AF: 0.272 Hom.: 2413

Bravo AF: 0.304

Asia WGS AF: 0.386 AC: 1338 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.97
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9368570; hg19: chr6-28676193;