16-55286589-A-G

Variant names:

• chr16-55286589-A-G
• rs30935
• ENST00000558730.2:n.89-3925T>C

Variant summary

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

The ENST00000558730.2(ENSG00000259283):​n.89-3925T>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 151,930 control chromosomes in the GnomAD database, including 12,014 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 (12014 hom., cov: 32)
• Consequence: ENSG00000259283 ENST00000558730.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0990
• 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=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.449 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
ENSG00000259283	ENST00000558730.2	n.89-3925T>C		intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes AF: 0.389 AC: 59076 AN: 151812 Hom.: 12009 Cov.: 32

Gnomad AFR AF: 0.244

Gnomad AMI AF: 0.398

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.414

Gnomad EAS AF: 0.449

Gnomad SAS AF: 0.460

Gnomad FIN AF: 0.416

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.447

Gnomad OTH AF: 0.392

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

GnomAD4 genome AF: 0.389 AC: 59103 AN: 151930 Hom.: 12014 Cov.: 32 AF XY: 0.392 AC XY: 29100 AN XY: 74286

African (AFR) AF: 0.244 AC: 10128 AN: 41466

American (AMR) AF: 0.458 AC: 6976 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.414 AC: 1437 AN: 3470

East Asian (EAS) AF: 0.448 AC: 2318 AN: 5172

South Asian (SAS) AF: 0.461 AC: 2222 AN: 4824

European-Finnish (FIN) AF: 0.416 AC: 4382 AN: 10532

Middle Eastern (MID) AF: 0.411 AC: 120 AN: 292

European-Non Finnish (NFE) AF: 0.447 AC: 30336 AN: 67918

Other (OTH) AF: 0.392 AC: 823 AN: 2102

Alfa AF: 0.424 Hom.: 7097

Bravo AF: 0.383

Asia WGS AF: 0.426 AC: 1483 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.94
DANN	Benign	0.83
PhyloP100		-0.099

Splicing

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

Other links and lift over

dbSNP: rs30935; hg19: chr16-55320501;