rs9910453

Positions:

• chr17-11027663-C-A
• chr17-11027663-C-G
• chr17-11027663-C-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 0.924 in 152,238 control chromosomes in the GnomAD database, including 65,109 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 0.92 (65109 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.194

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.924 AC: 140576 AN: 152120 Hom.: 65053 Cov.: 32

Gnomad AFR AF: 0.968

Gnomad AMI AF: 0.854

Gnomad AMR AF: 0.934

Gnomad ASJ AF: 0.884

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.855

Gnomad FIN AF: 0.922

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.899

Gnomad OTH AF: 0.906

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

GnomAD4 genome AF: 0.924 AC: 140691 AN: 152238 Hom.: 65109 Cov.: 32 AF XY: 0.925 AC XY: 68838 AN XY: 74428

Gnomad4 AFR AF: 0.968

Gnomad4 AMR AF: 0.934

Gnomad4 ASJ AF: 0.884

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.855

Gnomad4 FIN AF: 0.922

Gnomad4 NFE AF: 0.899

Gnomad4 OTH AF: 0.906

Alfa AF: 0.915 Hom.: 7973

Bravo AF: 0.929

Asia WGS AF: 0.935 AC: 3252 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.6
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9910453; hg19: chr17-10930980;