16-59114038-C-T

Position:

• chr16-59114038-C-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 0.365 in 151,992 control chromosomes in the GnomAD database, including 12,395 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 0.37 (12395 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.269

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.537 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.59114038C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000245768	ENST00000657379.1	n.720+49787C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.365 AC: 55505 AN: 151876 Hom.: 12395 Cov.: 32

Gnomad AFR AF: 0.0985

Gnomad AMI AF: 0.542

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.554

Gnomad FIN AF: 0.486

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.365 AC: 55503 AN: 151992 Hom.: 12395 Cov.: 32 AF XY: 0.369 AC XY: 27414 AN XY: 74296

Gnomad4 AFR AF: 0.0984

Gnomad4 AMR AF: 0.376

Gnomad4 ASJ AF: 0.343

Gnomad4 EAS AF: 0.410

Gnomad4 SAS AF: 0.555

Gnomad4 FIN AF: 0.486

Gnomad4 NFE AF: 0.488

Gnomad4 OTH AF: 0.376

Alfa AF: 0.430 Hom.: 6864

Bravo AF: 0.341

Asia WGS AF: 0.404 AC: 1404 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.2
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4238802; hg19: chr16-59147942;