rs4787427

chr16-27375073-C-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 0.757 in 152,084 control chromosomes in the GnomAD database, including 44,521 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 0.76 (44521 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.190

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.919 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.756 AC: 114922 AN: 151966 Hom.: 44449 Cov.: 31

Gnomad AFR AF: 0.927

Gnomad AMI AF: 0.746

Gnomad AMR AF: 0.768

Gnomad ASJ AF: 0.537

Gnomad EAS AF: 0.694

Gnomad SAS AF: 0.676

Gnomad FIN AF: 0.689

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.684

Gnomad OTH AF: 0.702

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

GnomAD4 genome AF: 0.757 AC: 115059 AN: 152084 Hom.: 44521 Cov.: 31 AF XY: 0.755 AC XY: 56126 AN XY: 74314

Gnomad4 AFR AF: 0.927

Gnomad4 AMR AF: 0.768

Gnomad4 ASJ AF: 0.537

Gnomad4 EAS AF: 0.694

Gnomad4 SAS AF: 0.677

Gnomad4 FIN AF: 0.689

Gnomad4 NFE AF: 0.684

Gnomad4 OTH AF: 0.705

Alfa AF: 0.733 Hom.: 5156

Bravo AF: 0.769

Asia WGS AF: 0.703 AC: 2447 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	3.3
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4787427; hg19: chr16-27386394;