chr16-55292892-A-G

Variant names:

• chr16-55292892-A-G
• rs11860394
• ENST00000558730.2:n.89-10228T>C

Variant summary

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

The ENST00000558730.2(ENSG00000259283):​n.89-10228T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.389 in 151,598 control chromosomes in the GnomAD database, including 11,803 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 0.39 (11803 hom., cov: 30)
• Consequence: ENSG00000259283 ENST00000558730.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.739
• Publications: 4 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.649 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000259283	ENST00000558730.2	TSL:3	n.89-10228T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.389 AC: 58910 AN: 151480 Hom.: 11790 Cov.: 30

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.669

Gnomad SAS AF: 0.467

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.354

Gnomad OTH AF: 0.379

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

GnomAD4 genome AF: 0.389 AC: 58964 AN: 151598 Hom.: 11803 Cov.: 30 AF XY: 0.393 AC XY: 29074 AN XY: 74026

African (AFR) AF: 0.410 AC: 16911 AN: 41280

American (AMR) AF: 0.379 AC: 5782 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.305 AC: 1058 AN: 3468

East Asian (EAS) AF: 0.668 AC: 3397 AN: 5084

South Asian (SAS) AF: 0.466 AC: 2234 AN: 4790

European-Finnish (FIN) AF: 0.406 AC: 4264 AN: 10498

Middle Eastern (MID) AF: 0.394 AC: 115 AN: 292

European-Non Finnish (NFE) AF: 0.354 AC: 24052 AN: 67908

Other (OTH) AF: 0.384 AC: 807 AN: 2104

Alfa AF: 0.366 Hom.: 45775

Bravo AF: 0.392

Asia WGS AF: 0.563 AC: 1958 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.42
DANN	Benign	0.64
PhyloP100		-0.74

Splicing

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

Other links and lift over

dbSNP: rs11860394; hg19: chr16-55326804;