16-58935607-T-G

Position:

• chr16-58935607-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 0.76 in 151,920 control chromosomes in the GnomAD database, including 44,157 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 0.76 (44157 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.837 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.58935607T>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000245768	ENST00000500117.1	n.680-128575T>G		intron_variant		2
ENSG00000245768	ENST00000657379.1	n.651-128575T>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.760 AC: 115311 AN: 151800 Hom.: 44127 Cov.: 31

Gnomad AFR AF: 0.701

Gnomad AMI AF: 0.899

Gnomad AMR AF: 0.708

Gnomad ASJ AF: 0.708

Gnomad EAS AF: 0.784

Gnomad SAS AF: 0.858

Gnomad FIN AF: 0.918

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.777

Gnomad OTH AF: 0.699

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

GnomAD4 genome AF: 0.760 AC: 115397 AN: 151920 Hom.: 44157 Cov.: 31 AF XY: 0.768 AC XY: 57020 AN XY: 74240

Gnomad4 AFR AF: 0.701

Gnomad4 AMR AF: 0.708

Gnomad4 ASJ AF: 0.708

Gnomad4 EAS AF: 0.785

Gnomad4 SAS AF: 0.859

Gnomad4 FIN AF: 0.918

Gnomad4 NFE AF: 0.777

Gnomad4 OTH AF: 0.700

Alfa AF: 0.763 Hom.: 72996

Bravo AF: 0.740

Asia WGS AF: 0.810 AC: 2817 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.090
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8049224; hg19: chr16-58969511;