chr16-55290182-A-G

Variant names:

• chr16-55290182-A-G
• rs733140
• ENST00000558730.2:n.89-7518T>C

Variant summary

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

The ENST00000558730.2(ENSG00000259283):​n.89-7518T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.266 in 152,074 control chromosomes in the GnomAD database, including 5,662 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 0.27 (5662 hom., cov: 32)
• Consequence: ENSG00000259283 ENST00000558730.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.297
• Publications: 2 publications found

Genes affected

ENSG00000259283 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.353 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000558730.2. 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
	ENSG00000259283	ENST00000558730.2	TSL:3	n.89-7518T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.266 AC: 40394 AN: 151956 Hom.: 5656 Cov.: 32

Gnomad AFR AF: 0.358

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.222

Gnomad EAS AF: 0.254

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.266 AC: 40410 AN: 152074 Hom.: 5662 Cov.: 32 AF XY: 0.264 AC XY: 19636 AN XY: 74330

African (AFR) AF: 0.358 AC: 14852 AN: 41456

American (AMR) AF: 0.176 AC: 2687 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.222 AC: 771 AN: 3472

East Asian (EAS) AF: 0.255 AC: 1317 AN: 5160

South Asian (SAS) AF: 0.273 AC: 1316 AN: 4824

European-Finnish (FIN) AF: 0.236 AC: 2500 AN: 10592

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.237 AC: 16129 AN: 67972

Other (OTH) AF: 0.243 AC: 513 AN: 2112

Alfa AF: 0.243 Hom.: 2596

Bravo AF: 0.263

Asia WGS AF: 0.242 AC: 840 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	8.6
DANN	Benign	0.90
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs733140; hg19: chr16-55324094;