rs224230

Variant names:

• chr16-3258357-G-A
• rs224230

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.927 AC: 38392 AN: 41396

American (AMR) AF: 0.702 AC: 10717 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.664 AC: 2306 AN: 3472

East Asian (EAS) AF: 0.675 AC: 3482 AN: 5160

South Asian (SAS) AF: 0.682 AC: 3282 AN: 4814

European-Finnish (FIN) AF: 0.658 AC: 6927 AN: 10532

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.649 AC: 44062 AN: 67932

Other (OTH) AF: 0.715 AC: 1505 AN: 2106

Alfa AF: 0.704 Hom.: 14810

Bravo AF: 0.743

Asia WGS AF: 0.719 AC: 2503 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.052
DANN	Benign	0.57
PhyloP100		-3.2

Splicing

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

Other links and lift over

dbSNP: rs224230; hg19: chr16-3308357;