rs4789932

Positions:

• chr17-78928193-G-A
• chr17-78928193-G-C

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 0.488 in 151,686 control chromosomes in the GnomAD database, including 18,493 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 0.49 (18493 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.71

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.638 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: 0.488 AC: 73931 AN: 151566 Hom.: 18448 Cov.: 30

Gnomad AFR AF: 0.569

Gnomad AMI AF: 0.459

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.444

Gnomad EAS AF: 0.656

Gnomad SAS AF: 0.569

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.404

Gnomad NFE AF: 0.442

Gnomad OTH AF: 0.462

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

GnomAD4 genome AF: 0.488 AC: 74040 AN: 151686 Hom.: 18493 Cov.: 30 AF XY: 0.485 AC XY: 35940 AN XY: 74120

Gnomad4 AFR AF: 0.569

Gnomad4 AMR AF: 0.496

Gnomad4 ASJ AF: 0.444

Gnomad4 EAS AF: 0.657

Gnomad4 SAS AF: 0.569

Gnomad4 FIN AF: 0.360

Gnomad4 NFE AF: 0.442

Gnomad4 OTH AF: 0.463

Alfa AF: 0.474 Hom.: 3062

Bravo AF: 0.502

Asia WGS AF: 0.624 AC: 2165 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.064
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4789932; hg19: chr17-76924275;