rs12933229

Variant names:

• chr16-29170869-T-C
• rs12933229
• ENST00000562902.2:n.298-46612T>C

Variant summary

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

The ENST00000562902.2(ENSG00000291188):​n.298-46612T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.256 in 152,210 control chromosomes in the GnomAD database, including 5,495 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 0.26 (5495 hom., cov: 33)
• Consequence: ENSG00000291188 ENST00000562902.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.65

Genes affected

ENSG00000291188 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.348 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
ENSG00000291188	ENST00000562902.2	n.298-46612T>C		intron_variant	Intron 2 of 2	2
ENSG00000260517	ENST00000563477.1	n.139+31070T>C		intron_variant	Intron 1 of 2	4
ENSG00000284685	ENST00000641956.1	n.421+31070T>C		intron_variant	Intron 1 of 7

Frequencies

GnomAD3 genomes AF: 0.256 AC: 38895 AN: 152092 Hom.: 5494 Cov.: 33

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.361

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.296

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

GnomAD4 genome AF: 0.256 AC: 38905 AN: 152210 Hom.: 5495 Cov.: 33 AF XY: 0.257 AC XY: 19095 AN XY: 74388

Gnomad4 AFR AF: 0.142

Gnomad4 AMR AF: 0.296

Gnomad4 ASJ AF: 0.305

Gnomad4 EAS AF: 0.362

Gnomad4 SAS AF: 0.183

Gnomad4 FIN AF: 0.317

Gnomad4 NFE AF: 0.301

Gnomad4 OTH AF: 0.297

Alfa AF: 0.296 Hom.: 9237

Bravo AF: 0.252

Asia WGS AF: 0.260 AC: 902 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.7
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: rs12933229; hg19: chr16-29182190;