16-55506915-G-T

Position:

• chr16-55506915-G-T

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 0.866 in 152,132 control chromosomes in the GnomAD database, including 57,903 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 0.87 (57903 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.105

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.936 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.866 AC: 131715 AN: 152014 Hom.: 57881 Cov.: 31

Gnomad AFR AF: 0.700

Gnomad AMI AF: 0.988

Gnomad AMR AF: 0.905

Gnomad ASJ AF: 0.863

Gnomad EAS AF: 0.869

Gnomad SAS AF: 0.864

Gnomad FIN AF: 0.966

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.942

Gnomad OTH AF: 0.879

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

GnomAD4 genome AF: 0.866 AC: 131780 AN: 152132 Hom.: 57903 Cov.: 31 AF XY: 0.866 AC XY: 64391 AN XY: 74376

Gnomad4 AFR AF: 0.699

Gnomad4 AMR AF: 0.905

Gnomad4 ASJ AF: 0.863

Gnomad4 EAS AF: 0.870

Gnomad4 SAS AF: 0.864

Gnomad4 FIN AF: 0.966

Gnomad4 NFE AF: 0.942

Gnomad4 OTH AF: 0.870

Alfa AF: 0.901 Hom.: 21397

Bravo AF: 0.856

Asia WGS AF: 0.804 AC: 2800 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	12
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs243831; hg19: chr16-55540827;