16-23055939-T-G

Position:

• chr16-23055939-T-G

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 0.812 in 152,178 control chromosomes in the GnomAD database, including 51,029 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 0.81 (51029 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.688

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.939 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.812 AC: 123503 AN: 152060 Hom.: 50978 Cov.: 31

Gnomad AFR AF: 0.947

Gnomad AMI AF: 0.750

Gnomad AMR AF: 0.618

Gnomad ASJ AF: 0.827

Gnomad EAS AF: 0.779

Gnomad SAS AF: 0.821

Gnomad FIN AF: 0.763

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.784

Gnomad OTH AF: 0.800

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

GnomAD4 genome AF: 0.812 AC: 123601 AN: 152178 Hom.: 51029 Cov.: 31 AF XY: 0.809 AC XY: 60178 AN XY: 74398

Gnomad4 AFR AF: 0.947

Gnomad4 AMR AF: 0.617

Gnomad4 ASJ AF: 0.827

Gnomad4 EAS AF: 0.779

Gnomad4 SAS AF: 0.819

Gnomad4 FIN AF: 0.763

Gnomad4 NFE AF: 0.784

Gnomad4 OTH AF: 0.802

Alfa AF: 0.787 Hom.: 52214

Bravo AF: 0.803

Asia WGS AF: 0.807 AC: 2810 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.62
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: rs8049603; hg19: chr16-23067260;