16-57355914-T-A

Variant names:

• chr16-57355914-T-A
• rs223886

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 0.628 in 151,654 control chromosomes in the GnomAD database, including 32,361 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 0.63 (32361 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.626
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.76 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: 0.628 AC: 95117 AN: 151536 Hom.: 32345 Cov.: 29

Gnomad AFR AF: 0.360

Gnomad AMI AF: 0.713

Gnomad AMR AF: 0.631

Gnomad ASJ AF: 0.720

Gnomad EAS AF: 0.532

Gnomad SAS AF: 0.525

Gnomad FIN AF: 0.838

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.765

Gnomad OTH AF: 0.649

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

GnomAD4 genome AF: 0.628 AC: 95172 AN: 151654 Hom.: 32361 Cov.: 29 AF XY: 0.626 AC XY: 46418 AN XY: 74096

African (AFR) AF: 0.360 AC: 14852 AN: 41292

American (AMR) AF: 0.631 AC: 9613 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.720 AC: 2489 AN: 3456

East Asian (EAS) AF: 0.532 AC: 2737 AN: 5146

South Asian (SAS) AF: 0.525 AC: 2523 AN: 4804

European-Finnish (FIN) AF: 0.838 AC: 8822 AN: 10532

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.765 AC: 51937 AN: 67886

Other (OTH) AF: 0.653 AC: 1369 AN: 2096

Alfa AF: 0.698 Hom.: 4623

Bravo AF: 0.603

Asia WGS AF: 0.518 AC: 1802 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.4
DANN	Benign	0.44
PhyloP100		0.63

Splicing

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

Other links and lift over

dbSNP: rs223886; hg19: chr16-57389826;