rs4467088

Variant names:

• chr16-20253984-G-C
• rs4467088
• ENST00000804517.1:n.83+1511C>G

Variant summary

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

The ENST00000804517.1(ENSG00000304556):​n.83+1511C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.806 in 152,174 control chromosomes in the GnomAD database, including 52,383 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 0.81 (52383 hom., cov: 33)
• Consequence: ENSG00000304556 ENST00000804517.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.116
• Publications: 5 publications found

Genes affected

ENSG00000304556 (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 (NFE) allele frequency at 95% confidence interval = 0.941 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
ENSG00000304556	ENST00000804517.1	n.83+1511C>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.806 AC: 122547 AN: 152056 Hom.: 52380 Cov.: 33

Gnomad AFR AF: 0.492

Gnomad AMI AF: 0.980

Gnomad AMR AF: 0.895

Gnomad ASJ AF: 0.889

Gnomad EAS AF: 0.759

Gnomad SAS AF: 0.890

Gnomad FIN AF: 0.921

Gnomad MID AF: 0.921

Gnomad NFE AF: 0.948

Gnomad OTH AF: 0.856

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

GnomAD4 genome AF: 0.806 AC: 122581 AN: 152174 Hom.: 52383 Cov.: 33 AF XY: 0.806 AC XY: 59997 AN XY: 74402

African (AFR) AF: 0.492 AC: 20378 AN: 41454

American (AMR) AF: 0.895 AC: 13695 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.889 AC: 3085 AN: 3472

East Asian (EAS) AF: 0.759 AC: 3920 AN: 5166

South Asian (SAS) AF: 0.890 AC: 4293 AN: 4824

European-Finnish (FIN) AF: 0.921 AC: 9773 AN: 10612

Middle Eastern (MID) AF: 0.922 AC: 271 AN: 294

European-Non Finnish (NFE) AF: 0.948 AC: 64463 AN: 68028

Other (OTH) AF: 0.857 AC: 1809 AN: 2112

Alfa AF: 0.868 Hom.: 7390

Bravo AF: 0.786

Asia WGS AF: 0.826 AC: 2870 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	0.98
DANN	Benign	0.60
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs4467088; hg19: chr16-20265306;