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. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.523 AC: 21694 AN: 41460

American (AMR) AF: 0.569 AC: 8688 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.660 AC: 2288 AN: 3468

East Asian (EAS) AF: 0.805 AC: 4164 AN: 5172

South Asian (SAS) AF: 0.595 AC: 2865 AN: 4812

European-Finnish (FIN) AF: 0.536 AC: 5651 AN: 10552

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.598 AC: 40672 AN: 67998

Other (OTH) AF: 0.603 AC: 1272 AN: 2108

Alfa AF: 0.593 Hom.: 48638

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
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs9396802; hg19: chr6-17755884;