rs9900808

Variant names:

• chr17-13159478-G-A
• rs9900808

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 0.0547 in 152,222 control chromosomes in the GnomAD database, including 308 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 0.055 (308 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.223

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0997 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: 0.0546 AC: 8308 AN: 152104 Hom.: 306 Cov.: 32

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0374

Gnomad ASJ AF: 0.0490

Gnomad EAS AF: 0.0596

Gnomad SAS AF: 0.0363

Gnomad FIN AF: 0.00754

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0387

Gnomad OTH AF: 0.0544

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

GnomAD4 genome AF: 0.0547 AC: 8329 AN: 152222 Hom.: 308 Cov.: 32 AF XY: 0.0531 AC XY: 3954 AN XY: 74422

Gnomad4 AFR AF: 0.102

Gnomad4 AMR AF: 0.0374

Gnomad4 ASJ AF: 0.0490

Gnomad4 EAS AF: 0.0597

Gnomad4 SAS AF: 0.0361

Gnomad4 FIN AF: 0.00754

Gnomad4 NFE AF: 0.0387

Gnomad4 OTH AF: 0.0539

Alfa AF: 0.0449 Hom.: 315

Bravo AF: 0.0596

Asia WGS AF: 0.0640 AC: 221 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.74
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9900808; hg19: chr17-13062795;