rs223830

Variant names:

• chr16-57418059-C-T
• rs223830

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 0.79 in 151,934 control chromosomes in the GnomAD database, including 48,230 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 0.79 (48230 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.473

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.915 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: 0.789 AC: 119847 AN: 151816 Hom.: 48180 Cov.: 29

Gnomad AFR AF: 0.923

Gnomad AMI AF: 0.758

Gnomad AMR AF: 0.683

Gnomad ASJ AF: 0.777

Gnomad EAS AF: 0.541

Gnomad SAS AF: 0.640

Gnomad FIN AF: 0.703

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.776

Gnomad OTH AF: 0.794

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

GnomAD4 genome AF: 0.790 AC: 119957 AN: 151934 Hom.: 48230 Cov.: 29 AF XY: 0.780 AC XY: 57911 AN XY: 74256

Gnomad4 AFR AF: 0.923

Gnomad4 AMR AF: 0.683

Gnomad4 ASJ AF: 0.777

Gnomad4 EAS AF: 0.540

Gnomad4 SAS AF: 0.641

Gnomad4 FIN AF: 0.703

Gnomad4 NFE AF: 0.776

Gnomad4 OTH AF: 0.796

Alfa AF: 0.784 Hom.: 5852

Bravo AF: 0.792

Asia WGS AF: 0.624 AC: 2172 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.1
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs223830; hg19: chr16-57451971;