rs9396802

Variant names:

• chr6-17755653-T-C
• rs9396802

Your query was ambiguous. Multiple possible variants found:

• chr6-17755653-T-C
• chr6-17755653-T-G

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 0.578 in 152,040 control chromosomes in the GnomAD database, including 25,646 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 0.58 (25646 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.69

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.785 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: 0.578 AC: 87784 AN: 151922 Hom.: 25621 Cov.: 32

Gnomad AFR AF: 0.523

Gnomad AMI AF: 0.431

Gnomad AMR AF: 0.569

Gnomad ASJ AF: 0.660

Gnomad EAS AF: 0.805

Gnomad SAS AF: 0.596

Gnomad FIN AF: 0.536

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.598

Gnomad OTH AF: 0.600

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

GnomAD4 genome AF: 0.578 AC: 87853 AN: 152040 Hom.: 25646 Cov.: 32 AF XY: 0.579 AC XY: 43029 AN XY: 74312

Gnomad4 AFR AF: 0.523

Gnomad4 AMR AF: 0.569

Gnomad4 ASJ AF: 0.660

Gnomad4 EAS AF: 0.805

Gnomad4 SAS AF: 0.595

Gnomad4 FIN AF: 0.536

Gnomad4 NFE AF: 0.598

Gnomad4 OTH AF: 0.603

Alfa AF: 0.594 Hom.: 34984

Bravo AF: 0.576

Asia WGS AF: 0.693 AC: 2411 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	0.54
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9396802; hg19: chr6-17755884;