chr6-102817684-G-A

Variant names:

• chr6-102817684-G-A
• rs9322676

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 0.153 in 151,626 control chromosomes in the GnomAD database, including 4,416 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 0.15 (4416 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.189
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.444 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23150 AN: 151508 Hom.: 4383 Cov.: 31

Gnomad AFR AF: 0.449

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.0326

Gnomad EAS AF: 0.0962

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.0269

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0214

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.153 AC: 23252 AN: 151626 Hom.: 4416 Cov.: 31 AF XY: 0.150 AC XY: 11122 AN XY: 74130

African (AFR) AF: 0.450 AC: 18562 AN: 41292

American (AMR) AF: 0.102 AC: 1554 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.0326 AC: 113 AN: 3466

East Asian (EAS) AF: 0.0966 AC: 499 AN: 5166

South Asian (SAS) AF: 0.109 AC: 523 AN: 4820

European-Finnish (FIN) AF: 0.0269 AC: 285 AN: 10582

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0214 AC: 1449 AN: 67758

Other (OTH) AF: 0.112 AC: 235 AN: 2104

Alfa AF: 0.0334 Hom.: 81

Bravo AF: 0.174

Asia WGS AF: 0.144 AC: 499 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.6
DANN	Benign	0.24
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs9322676; hg19: chr6-103265559;