rs8043884

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr16-64549363-C-A
• chr16-64549363-C-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000259846 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

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
ENSG00000259846	ENST00000564046.1	n.439+14287C>A		intron_variant	Intron 4 of 4	4

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

Gnomad4 AFR AF: 0.188

Gnomad4 AMR AF: 0.202

Gnomad4 ASJ AF: 0.270

Gnomad4 EAS AF: 0.00601

Gnomad4 SAS AF: 0.238

Gnomad4 FIN AF: 0.256

Gnomad4 NFE AF: 0.272

Gnomad4 OTH AF: 0.220

Alfa AF: 0.152 Hom.: 345

Bravo AF: 0.224

Asia WGS AF: 0.126 AC: 440 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8043884; hg19: chr16-64583266;