rs4789400

Variant names:

• chr17-77001815-A-G
• rs4789400

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 0.949 in 152,256 control chromosomes in the GnomAD database, including 68,601 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 0.95 (68601 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.84

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.971 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: 0.949 AC: 144353 AN: 152138 Hom.: 68549 Cov.: 31

Gnomad AFR AF: 0.919

Gnomad AMI AF: 0.973

Gnomad AMR AF: 0.972

Gnomad ASJ AF: 0.946

Gnomad EAS AF: 0.994

Gnomad SAS AF: 0.949

Gnomad FIN AF: 0.992

Gnomad MID AF: 0.921

Gnomad NFE AF: 0.952

Gnomad OTH AF: 0.944

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

GnomAD4 genome AF: 0.949 AC: 144465 AN: 152256 Hom.: 68601 Cov.: 31 AF XY: 0.952 AC XY: 70910 AN XY: 74464

Gnomad4 AFR AF: 0.919

Gnomad4 AMR AF: 0.972

Gnomad4 ASJ AF: 0.946

Gnomad4 EAS AF: 0.993

Gnomad4 SAS AF: 0.949

Gnomad4 FIN AF: 0.992

Gnomad4 NFE AF: 0.952

Gnomad4 OTH AF: 0.945

Alfa AF: 0.950 Hom.: 33623

Bravo AF: 0.947

Asia WGS AF: 0.970 AC: 3375 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.36
DANN	Benign	0.15

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4789400; hg19: chr17-74997897;