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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.394 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

Gnomad4 AFR AF: 0.310

Gnomad4 AMR AF: 0.466

Gnomad4 ASJ AF: 0.363

Gnomad4 EAS AF: 0.341

Gnomad4 SAS AF: 0.433

Gnomad4 FIN AF: 0.465

Gnomad4 NFE AF: 0.421

Gnomad4 OTH AF: 0.398

Alfa AF: 0.418 Hom.: 11229

Bravo AF: 0.387

Asia WGS AF: 0.457 AC: 1590 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

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