rs9906760

Variant names:

• chr17-4375540-A-G
• rs9906760

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 0.426 in 151,876 control chromosomes in the GnomAD database, including 15,256 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 0.43 (15256 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.635 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: 0.426 AC: 64597 AN: 151758 Hom.: 15206 Cov.: 31

Gnomad AFR AF: 0.641

Gnomad AMI AF: 0.342

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.202

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.379

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.397

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

GnomAD4 genome AF: 0.426 AC: 64707 AN: 151876 Hom.: 15256 Cov.: 31 AF XY: 0.426 AC XY: 31582 AN XY: 74214

Gnomad4 AFR AF: 0.641

Gnomad4 AMR AF: 0.422

Gnomad4 ASJ AF: 0.301

Gnomad4 EAS AF: 0.202

Gnomad4 SAS AF: 0.380

Gnomad4 FIN AF: 0.379

Gnomad4 NFE AF: 0.332

Gnomad4 OTH AF: 0.401

Alfa AF: 0.346 Hom.: 18067

Bravo AF: 0.440

Asia WGS AF: 0.347 AC: 1206 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.73
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9906760; hg19: chr17-4278835;