rs9356206

Variant names:

• chr6-164397801-G-A
• rs9356206

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 0.0797 in 152,182 control chromosomes in the GnomAD database, including 652 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 0.080 (652 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.582

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.134 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0796 AC: 12100 AN: 152064 Hom.: 649 Cov.: 32

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.0835

Gnomad AMR AF: 0.0569

Gnomad ASJ AF: 0.0392

Gnomad EAS AF: 0.0943

Gnomad SAS AF: 0.0774

Gnomad FIN AF: 0.0230

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0601

Gnomad OTH AF: 0.0670

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

GnomAD4 genome AF: 0.0797 AC: 12124 AN: 152182 Hom.: 652 Cov.: 32 AF XY: 0.0785 AC XY: 5843 AN XY: 74420

Gnomad4 AFR AF: 0.137

Gnomad4 AMR AF: 0.0568

Gnomad4 ASJ AF: 0.0392

Gnomad4 EAS AF: 0.0943

Gnomad4 SAS AF: 0.0770

Gnomad4 FIN AF: 0.0230

Gnomad4 NFE AF: 0.0601

Gnomad4 OTH AF: 0.0672

Alfa AF: 0.0618 Hom.: 414

Bravo AF: 0.0838

Asia WGS AF: 0.117 AC: 406 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.93
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9356206; hg19: chr6-164818834;