rs223887

Variant names:

• chr16-57357302-G-T
• rs223887

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 0.675 in 148,730 control chromosomes in the GnomAD database, including 34,991 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 0.67 (34991 hom., cov: 24)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.369

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.765 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: 0.675 AC: 100256 AN: 148616 Hom.: 34957 Cov.: 24

Gnomad AFR AF: 0.495

Gnomad AMI AF: 0.715

Gnomad AMR AF: 0.667

Gnomad ASJ AF: 0.768

Gnomad EAS AF: 0.536

Gnomad SAS AF: 0.533

Gnomad FIN AF: 0.844

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.771

Gnomad OTH AF: 0.701

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

GnomAD4 genome AF: 0.675 AC: 100346 AN: 148730 Hom.: 34991 Cov.: 24 AF XY: 0.674 AC XY: 48826 AN XY: 72478

Gnomad4 AFR AF: 0.495

Gnomad4 AMR AF: 0.667

Gnomad4 ASJ AF: 0.768

Gnomad4 EAS AF: 0.536

Gnomad4 SAS AF: 0.534

Gnomad4 FIN AF: 0.844

Gnomad4 NFE AF: 0.771

Gnomad4 OTH AF: 0.705

Alfa AF: 0.725 Hom.: 5083

Bravo AF: 0.650

Asia WGS AF: 0.531 AC: 1850 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.66
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs223887; hg19: chr16-57391214;