rs224230

Variant names:

• chr16-3258357-G-A
• rs224230

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;