16-53507186-C-T

Variant names:

• chr16-53507186-C-T
• rs3095635
• ENST00000790323.1:n.89-2479C>T

Variant summary

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

The ENST00000790323.1(ENSG00000302896):​n.89-2479C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.825 in 152,218 control chromosomes in the GnomAD database, including 52,016 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 0.83 (52016 hom., cov: 33)
• Consequence: ENSG00000302896 ENST00000790323.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.629
• Publications: 10 publications found

Genes affected

ENSG00000302896 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.862 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000790323.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000302896	ENST00000790323.1		n.89-2479C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.825 AC: 125541 AN: 152100 Hom.: 51972 Cov.: 33

Gnomad AFR AF: 0.860

Gnomad AMI AF: 0.769

Gnomad AMR AF: 0.822

Gnomad ASJ AF: 0.864

Gnomad EAS AF: 0.884

Gnomad SAS AF: 0.798

Gnomad FIN AF: 0.719

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.817

Gnomad OTH AF: 0.831

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

GnomAD4 genome AF: 0.825 AC: 125642 AN: 152218 Hom.: 52016 Cov.: 33 AF XY: 0.822 AC XY: 61135 AN XY: 74412

African (AFR) AF: 0.860 AC: 35742 AN: 41540

American (AMR) AF: 0.822 AC: 12565 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.864 AC: 3000 AN: 3472

East Asian (EAS) AF: 0.884 AC: 4578 AN: 5180

South Asian (SAS) AF: 0.797 AC: 3843 AN: 4820

European-Finnish (FIN) AF: 0.719 AC: 7611 AN: 10582

Middle Eastern (MID) AF: 0.827 AC: 243 AN: 294

European-Non Finnish (NFE) AF: 0.817 AC: 55597 AN: 68014

Other (OTH) AF: 0.833 AC: 1762 AN: 2114

Alfa AF: 0.822 Hom.: 101187

Bravo AF: 0.835

Asia WGS AF: 0.849 AC: 2954 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.49
DANN	Benign	0.47
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs3095635; hg19: chr16-53541098;