rs16884711

Variant names:

• chr5-56028975-A-C
• rs16884711
• ENST00000645512.1:n.279+34774A>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000645512.1(ENSG00000249236):​n.279+34774A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.189 in 152,108 control chromosomes in the GnomAD database, including 2,783 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 0.19 (2783 hom., cov: 32)
• Consequence: ENSG00000249236 ENST00000645512.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.68

Genes affected

ENSG00000249236 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.245 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
ENSG00000249236	ENST00000645512.1	n.279+34774A>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.189 AC: 28686 AN: 151990 Hom.: 2779 Cov.: 32

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.0627

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.189 AC: 28710 AN: 152108 Hom.: 2783 Cov.: 32 AF XY: 0.185 AC XY: 13797 AN XY: 74386

Gnomad4 AFR AF: 0.188

Gnomad4 AMR AF: 0.168

Gnomad4 ASJ AF: 0.209

Gnomad4 EAS AF: 0.0626

Gnomad4 SAS AF: 0.257

Gnomad4 FIN AF: 0.180

Gnomad4 NFE AF: 0.198

Gnomad4 OTH AF: 0.204

Alfa AF: 0.198 Hom.: 1795

Bravo AF: 0.186

Asia WGS AF: 0.158 AC: 551 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.8
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16884711; hg19: chr5-55324802;