16-58935607-T-G

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000245768 (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 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

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;