rs9268516

Variant names:

• chr6-32411712-C-T
• rs9268516

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 0.24 in 152,170 control chromosomes in the GnomAD database, including 4,590 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 0.24 (4590 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.372
• Publications: 59 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.287 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: 0.240 AC: 36454 AN: 152052 Hom.: 4591 Cov.: 33

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.213

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.240 AC: 36467 AN: 152170 Hom.: 4590 Cov.: 33 AF XY: 0.236 AC XY: 17531 AN XY: 74392

African (AFR) AF: 0.183 AC: 7594 AN: 41514

American (AMR) AF: 0.295 AC: 4506 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.305 AC: 1057 AN: 3470

East Asian (EAS) AF: 0.148 AC: 766 AN: 5182

South Asian (SAS) AF: 0.231 AC: 1113 AN: 4826

European-Finnish (FIN) AF: 0.185 AC: 1963 AN: 10592

Middle Eastern (MID) AF: 0.209 AC: 61 AN: 292

European-Non Finnish (NFE) AF: 0.275 AC: 18686 AN: 67976

Other (OTH) AF: 0.232 AC: 491 AN: 2112

Alfa AF: 0.269 Hom.: 14376

Bravo AF: 0.253

Asia WGS AF: 0.163 AC: 568 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.4
DANN	Benign	0.69
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs9268516; hg19: chr6-32379489;