chr16-17840448-A-C

Variant names:

• chr16-17840448-A-C
• rs1389504
• ENST00000824815.1:n.247-8585T>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000824815.1(ENSG00000259929):​n.247-8585T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.737 in 151,814 control chromosomes in the GnomAD database, including 42,075 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 0.74 (42075 hom., cov: 30)
• Consequence: ENSG00000259929 ENST00000824815.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.566
• Publications: 4 publications found

Genes affected

ENSG00000259929 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.31).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.888 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000259929	ENST00000824815.1		n.247-8585T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.737 AC: 111766 AN: 151698 Hom.: 42019 Cov.: 30

Gnomad AFR AF: 0.896

Gnomad AMI AF: 0.581

Gnomad AMR AF: 0.732

Gnomad ASJ AF: 0.797

Gnomad EAS AF: 0.781

Gnomad SAS AF: 0.729

Gnomad FIN AF: 0.650

Gnomad MID AF: 0.780

Gnomad NFE AF: 0.650

Gnomad OTH AF: 0.750

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

GnomAD4 genome AF: 0.737 AC: 111880 AN: 151814 Hom.: 42075 Cov.: 30 AF XY: 0.737 AC XY: 54696 AN XY: 74166

African (AFR) AF: 0.896 AC: 37067 AN: 41384

American (AMR) AF: 0.733 AC: 11185 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.797 AC: 2756 AN: 3460

East Asian (EAS) AF: 0.781 AC: 4022 AN: 5150

South Asian (SAS) AF: 0.728 AC: 3497 AN: 4802

European-Finnish (FIN) AF: 0.650 AC: 6830 AN: 10510

Middle Eastern (MID) AF: 0.784 AC: 229 AN: 292

European-Non Finnish (NFE) AF: 0.650 AC: 44179 AN: 67934

Other (OTH) AF: 0.753 AC: 1586 AN: 2106

Alfa AF: 0.692 Hom.: 58069

Bravo AF: 0.748

Asia WGS AF: 0.775 AC: 2691 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.31
CADD	Benign	18
DANN	Benign	0.67
PhyloP100		0.57

Splicing

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

Other links and lift over

dbSNP: rs1389504; hg19: chr16-17934305;