16-56856988-G-T

Variant names:

• chr16-56856988-G-T
• rs1529930

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 0.879 in 152,124 control chromosomes in the GnomAD database, including 59,096 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 0.88 (59096 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0190

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.972 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: 0.879 AC: 133611 AN: 152006 Hom.: 59039 Cov.: 30

Gnomad AFR AF: 0.961

Gnomad AMI AF: 0.889

Gnomad AMR AF: 0.913

Gnomad ASJ AF: 0.836

Gnomad EAS AF: 0.995

Gnomad SAS AF: 0.933

Gnomad FIN AF: 0.801

Gnomad MID AF: 0.918

Gnomad NFE AF: 0.823

Gnomad OTH AF: 0.876

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

GnomAD4 genome AF: 0.879 AC: 133727 AN: 152124 Hom.: 59096 Cov.: 30 AF XY: 0.882 AC XY: 65598 AN XY: 74380

Gnomad4 AFR AF: 0.961

Gnomad4 AMR AF: 0.913

Gnomad4 ASJ AF: 0.836

Gnomad4 EAS AF: 0.995

Gnomad4 SAS AF: 0.932

Gnomad4 FIN AF: 0.801

Gnomad4 NFE AF: 0.823

Gnomad4 OTH AF: 0.879

Alfa AF: 0.854 Hom.: 9402

Bravo AF: 0.892

Asia WGS AF: 0.958 AC: 3331 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.1
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1529930; hg19: chr16-56890900;