rs16922328

Variant names:

• chr11-95648004-C-T
• rs16922328
• ENST00000648353.1:n.525+75796C>T

Variant summary

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

The ENST00000648353.1(ENSG00000285842):​n.525+75796C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.152 in 152,058 control chromosomes in the GnomAD database, including 1,778 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 0.15 (1778 hom., cov: 32)
• Consequence: ENSG00000285842 ENST00000648353.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.125

Genes affected

ENSG00000285842 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.199 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
ENSG00000285842	ENST00000648353.1	n.525+75796C>T		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.152 AC: 23068 AN: 151940 Hom.: 1780 Cov.: 32

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.0469

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.152 AC: 23077 AN: 152058 Hom.: 1778 Cov.: 32 AF XY: 0.154 AC XY: 11458 AN XY: 74338

Gnomad4 AFR AF: 0.187

Gnomad4 AMR AF: 0.155

Gnomad4 ASJ AF: 0.186

Gnomad4 EAS AF: 0.0456

Gnomad4 SAS AF: 0.209

Gnomad4 FIN AF: 0.161

Gnomad4 NFE AF: 0.132

Gnomad4 OTH AF: 0.143

Alfa AF: 0.0872 Hom.: 192

Bravo AF: 0.151

Asia WGS AF: 0.130 AC: 453 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.9
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16922328; hg19: chr11-95381168;