chr16-64549363-C-A

Variant names:

• chr16-64549363-C-A
• rs8043884
• ENST00000564046.1:n.439+14287C>A

Variant summary

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

The ENST00000564046.1(ENSG00000259846):​n.439+14287C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.23 in 151,976 control chromosomes in the GnomAD database, including 4,244 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 0.23 (4244 hom., cov: 32)
• Consequence: ENSG00000259846 ENST00000564046.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• Publications: 4 publications found

Genes affected

ENSG00000259846 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.269 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000564046.1. 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
	ENSG00000259846	ENST00000564046.1	TSL:4	n.439+14287C>A		intron	N/A
	ENSG00000259846	ENST00000808892.1		n.418-50776C>A		intron	N/A
	ENSG00000259846	ENST00000808893.1		n.404-50776C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.230 AC: 34994 AN: 151858 Hom.: 4244 Cov.: 32

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.00581

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.256

Gnomad MID AF: 0.223

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.230 AC: 35003 AN: 151976 Hom.: 4244 Cov.: 32 AF XY: 0.228 AC XY: 16932 AN XY: 74284

African (AFR) AF: 0.188 AC: 7778 AN: 41450

American (AMR) AF: 0.202 AC: 3082 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.270 AC: 938 AN: 3470

East Asian (EAS) AF: 0.00601 AC: 31 AN: 5154

South Asian (SAS) AF: 0.238 AC: 1144 AN: 4814

European-Finnish (FIN) AF: 0.256 AC: 2699 AN: 10540

Middle Eastern (MID) AF: 0.219 AC: 64 AN: 292

European-Non Finnish (NFE) AF: 0.272 AC: 18498 AN: 67984

Other (OTH) AF: 0.220 AC: 463 AN: 2108

Alfa AF: 0.155 Hom.: 363

Bravo AF: 0.224

Asia WGS AF: 0.126 AC: 440 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.092
DANN	Benign	0.46
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs8043884; hg19: chr16-64583266;