rs9910408

Variant names:

• chr17-47725508-A-G
• rs9910408

Your query was ambiguous. Multiple possible variants found:

• chr17-47725508-A-G
• chr17-47725508-A-T

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 0.394 in 151,770 control chromosomes in the GnomAD database, including 12,177 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 0.39 (12177 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.789
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.457 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: 0.394 AC: 59817 AN: 151652 Hom.: 12175 Cov.: 31

Gnomad AFR AF: 0.310

Gnomad AMI AF: 0.405

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.341

Gnomad SAS AF: 0.434

Gnomad FIN AF: 0.465

Gnomad MID AF: 0.397

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.396

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

GnomAD4 genome AF: 0.394 AC: 59843 AN: 151770 Hom.: 12177 Cov.: 31 AF XY: 0.399 AC XY: 29591 AN XY: 74158

African (AFR) AF: 0.310 AC: 12819 AN: 41368

American (AMR) AF: 0.466 AC: 7113 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.363 AC: 1259 AN: 3466

East Asian (EAS) AF: 0.341 AC: 1753 AN: 5138

South Asian (SAS) AF: 0.433 AC: 2072 AN: 4790

European-Finnish (FIN) AF: 0.465 AC: 4906 AN: 10558

Middle Eastern (MID) AF: 0.386 AC: 112 AN: 290

European-Non Finnish (NFE) AF: 0.421 AC: 28606 AN: 67894

Other (OTH) AF: 0.398 AC: 836 AN: 2102

Alfa AF: 0.417 Hom.: 13314

Bravo AF: 0.387

Asia WGS AF: 0.457 AC: 1590 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	12
DANN	Benign	0.62
PhyloP100		0.79

Splicing

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

Other links and lift over

dbSNP: rs9910408; hg19: chr17-45802874; COSMIC: COSV55557543;