rs224230

chr16-3258357-G-A

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 0.733 in 151,872 control chromosomes in the GnomAD database, including 42,018 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 0.73 (42018 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.22

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 (AFR) allele frequency at 95% confidence interval = 0.92 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: 0.733 AC: 111191 AN: 151754 Hom.: 41955 Cov.: 30

Gnomad AFR AF: 0.927

Gnomad AMI AF: 0.517

Gnomad AMR AF: 0.702

Gnomad ASJ AF: 0.664

Gnomad EAS AF: 0.676

Gnomad SAS AF: 0.682

Gnomad FIN AF: 0.658

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.649

Gnomad OTH AF: 0.714

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

GnomAD4 genome AF: 0.733 AC: 111313 AN: 151872 Hom.: 42018 Cov.: 30 AF XY: 0.731 AC XY: 54231 AN XY: 74200

Gnomad4 AFR AF: 0.927

Gnomad4 AMR AF: 0.702

Gnomad4 ASJ AF: 0.664

Gnomad4 EAS AF: 0.675

Gnomad4 SAS AF: 0.682

Gnomad4 FIN AF: 0.658

Gnomad4 NFE AF: 0.649

Gnomad4 OTH AF: 0.715

Alfa AF: 0.710 Hom.: 8627

Bravo AF: 0.743

Asia WGS AF: 0.719 AC: 2503 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	0.052
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: rs224230; hg19: chr16-3308357;