rs4789400

Positions:

• chr17-77001815-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 0.949 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;