rs9906760

chr17-4375540-A-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;