16-17899373-A-G

Variant names:

• chr16-17899373-A-G
• rs9937528
• ENST00000824815.1:n.147-38184T>C

Variant summary

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

The ENST00000824815.1(ENSG00000259929):​n.147-38184T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.453 in 152,038 control chromosomes in the GnomAD database, including 15,700 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 0.45 (15700 hom., cov: 32)
• Consequence: ENSG00000259929 ENST00000824815.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.839
• Publications: 3 publications found

Genes affected

ENSG00000259929 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.461 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000824815.1. 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
	ENSG00000259929	ENST00000824815.1		n.147-38184T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.453 AC: 68808 AN: 151920 Hom.: 15687 Cov.: 32

Gnomad AFR AF: 0.467

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.429

Gnomad ASJ AF: 0.591

Gnomad EAS AF: 0.466

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.469

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.447

Gnomad OTH AF: 0.468

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

GnomAD4 genome AF: 0.453 AC: 68858 AN: 152038 Hom.: 15700 Cov.: 32 AF XY: 0.454 AC XY: 33725 AN XY: 74330

African (AFR) AF: 0.467 AC: 19357 AN: 41478

American (AMR) AF: 0.429 AC: 6541 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.591 AC: 2049 AN: 3468

East Asian (EAS) AF: 0.467 AC: 2408 AN: 5158

South Asian (SAS) AF: 0.369 AC: 1779 AN: 4826

European-Finnish (FIN) AF: 0.469 AC: 4959 AN: 10566

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.447 AC: 30360 AN: 67968

Other (OTH) AF: 0.473 AC: 997 AN: 2106

Alfa AF: 0.438 Hom.: 2545

Bravo AF: 0.453

Asia WGS AF: 0.419 AC: 1461 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.50
DANN	Benign	0.55
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs9937528; hg19: chr16-17993230;