16-59358116-T-C

Position:

• chr16-59358116-T-C

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 0.111 in 152,194 control chromosomes in the GnomAD database, including 1,836 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 0.11 (1836 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.79

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.381 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.59358116T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16790 AN: 152076 Hom.: 1833 Cov.: 32

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0751

Gnomad ASJ AF: 0.0458

Gnomad EAS AF: 0.395

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.0399

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0251

Gnomad OTH AF: 0.0995

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

GnomAD4 genome AF: 0.111 AC: 16823 AN: 152194 Hom.: 1836 Cov.: 32 AF XY: 0.114 AC XY: 8518 AN XY: 74410

Gnomad4 AFR AF: 0.241

Gnomad4 AMR AF: 0.0752

Gnomad4 ASJ AF: 0.0458

Gnomad4 EAS AF: 0.395

Gnomad4 SAS AF: 0.228

Gnomad4 FIN AF: 0.0399

Gnomad4 NFE AF: 0.0251

Gnomad4 OTH AF: 0.100

Alfa AF: 0.0323 Hom.: 52

Bravo AF: 0.119

Asia WGS AF: 0.263 AC: 918 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.34
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9939608; hg19: chr16-59392020;