rs9469240

Variant names:

• chr6-32722224-C-T
• rs9469240

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 0.377 in 151,748 control chromosomes in the GnomAD database, including 12,036 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 0.38 (12036 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.264
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.598 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.377 AC: 57234 AN: 151628 Hom.: 12026 Cov.: 31

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.670

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.617

Gnomad SAS AF: 0.491

Gnomad FIN AF: 0.538

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.412

Gnomad OTH AF: 0.368

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

GnomAD4 genome AF: 0.377 AC: 57277 AN: 151748 Hom.: 12036 Cov.: 31 AF XY: 0.386 AC XY: 28625 AN XY: 74158

African (AFR) AF: 0.206 AC: 8529 AN: 41366

American (AMR) AF: 0.438 AC: 6671 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.390 AC: 1354 AN: 3468

East Asian (EAS) AF: 0.616 AC: 3184 AN: 5166

South Asian (SAS) AF: 0.490 AC: 2362 AN: 4818

European-Finnish (FIN) AF: 0.538 AC: 5648 AN: 10496

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.412 AC: 27984 AN: 67878

Other (OTH) AF: 0.377 AC: 796 AN: 2110

Alfa AF: 0.380 Hom.: 1944

Bravo AF: 0.364

Asia WGS AF: 0.545 AC: 1892 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	8.1
DANN	Benign	0.45
PhyloP100		-0.26

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9469240; hg19: chr6-32690001;