rs8058794

Variant names:

• chr16-16816964-C-T
• rs8058794
• ENST00000787165.1:n.119-16666C>T

Variant summary

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

The ENST00000787165.1(ENSG00000302475):​n.119-16666C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.121 in 152,188 control chromosomes in the GnomAD database, including 1,196 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 0.12 (1196 hom., cov: 32)
• Consequence: ENSG00000302475 ENST00000787165.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640
• Publications: 1 publications found

Genes affected

ENSG00000302475 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.146 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
ENSG00000302475	ENST00000787165.1	n.119-16666C>T		intron_variant	Intron 2 of 3
ENSG00000302475	ENST00000787171.1	n.187+9821C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.122 AC: 18493 AN: 152070 Hom.: 1195 Cov.: 32

Gnomad AFR AF: 0.0941

Gnomad AMI AF: 0.0989

Gnomad AMR AF: 0.0911

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.0162

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.121 AC: 18487 AN: 152188 Hom.: 1196 Cov.: 32 AF XY: 0.120 AC XY: 8922 AN XY: 74392

African (AFR) AF: 0.0938 AC: 3898 AN: 41536

American (AMR) AF: 0.0909 AC: 1390 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.151 AC: 523 AN: 3470

East Asian (EAS) AF: 0.0162 AC: 84 AN: 5176

South Asian (SAS) AF: 0.153 AC: 738 AN: 4812

European-Finnish (FIN) AF: 0.133 AC: 1405 AN: 10584

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.148 AC: 10067 AN: 68000

Other (OTH) AF: 0.123 AC: 260 AN: 2116

Alfa AF: 0.135 Hom.: 2733

Bravo AF: 0.116

Asia WGS AF: 0.0720 AC: 248 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.0
DANN	Benign	0.63
PhyloP100		0.064

Splicing

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

Other links and lift over

dbSNP: rs8058794; hg19: chr16-16910821;