rs4789400

Variant names:

• chr17-77001815-A-G
• rs4789400

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.919 AC: 38153 AN: 41528

American (AMR) AF: 0.972 AC: 14868 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.946 AC: 3284 AN: 3470

East Asian (EAS) AF: 0.993 AC: 5144 AN: 5178

South Asian (SAS) AF: 0.949 AC: 4578 AN: 4826

European-Finnish (FIN) AF: 0.992 AC: 10535 AN: 10620

Middle Eastern (MID) AF: 0.922 AC: 271 AN: 294

European-Non Finnish (NFE) AF: 0.952 AC: 64749 AN: 68018

Other (OTH) AF: 0.945 AC: 1996 AN: 2112

Alfa AF: 0.949 Hom.: 91577

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
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs4789400; hg19: chr17-74997897;