16-58935607-T-G

Variant names:

• chr16-58935607-T-G
• rs8049224
• ENST00000500117.1:n.680-128575T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000500117.1(ENSG00000245768):​n.680-128575T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000245768 ENST00000500117.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37
• Publications: 3 publications found

Genes affected

ENSG00000245768 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000245768	ENST00000500117.1	n.680-128575T>G		intron_variant	Intron 2 of 3	2
ENSG00000245768	ENST00000657379.1	n.651-128575T>G		intron_variant	Intron 2 of 3

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

African (AFR) AF: 0.701 AC: 29044 AN: 41428

American (AMR) AF: 0.708 AC: 10800 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.708 AC: 2454 AN: 3466

East Asian (EAS) AF: 0.785 AC: 4047 AN: 5158

South Asian (SAS) AF: 0.859 AC: 4139 AN: 4820

European-Finnish (FIN) AF: 0.918 AC: 9666 AN: 10532

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.777 AC: 52767 AN: 67952

Other (OTH) AF: 0.700 AC: 1475 AN: 2108

Alfa AF: 0.765 Hom.: 168638

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
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs8049224; hg19: chr16-58969511;