rs4787924

Variant names:

• chr16-24253217-G-A
• rs4787924

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 0.532 in 151,934 control chromosomes in the GnomAD database, including 21,628 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 0.53 (21628 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.314

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.579 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: 0.532 AC: 80760 AN: 151818 Hom.: 21605 Cov.: 31

Gnomad AFR AF: 0.549

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.530

Gnomad ASJ AF: 0.534

Gnomad EAS AF: 0.385

Gnomad SAS AF: 0.598

Gnomad FIN AF: 0.536

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.531

Gnomad OTH AF: 0.526

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

GnomAD4 genome AF: 0.532 AC: 80834 AN: 151934 Hom.: 21628 Cov.: 31 AF XY: 0.534 AC XY: 39636 AN XY: 74276

Gnomad4 AFR AF: 0.549

Gnomad4 AMR AF: 0.530

Gnomad4 ASJ AF: 0.534

Gnomad4 EAS AF: 0.387

Gnomad4 SAS AF: 0.598

Gnomad4 FIN AF: 0.536

Gnomad4 NFE AF: 0.531

Gnomad4 OTH AF: 0.526

Alfa AF: 0.530 Hom.: 43915

Bravo AF: 0.529

Asia WGS AF: 0.528 AC: 1835 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.5
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4787924; hg19: chr16-24264538;