rs12933229

chr16-29170869-T-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, non coding transcript 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: ENST00000562902.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.65

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000562902.2	n.298-46612T>C		intron_variant, non_coding_transcript_variant		2
	ENST00000563477.1	n.139+31070T>C		intron_variant, non_coding_transcript_variant		4
	ENST00000691488.1	n.80+13515T>C		intron_variant, non_coding_transcript_variant
	ENST00000702506.1	n.612+15984T>C		intron_variant, non_coding_transcript_variant

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;