rs12579003

Positions:

• chr12-89768083-C-T

Variant summary

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

The ENST00000651272.1(ENSG00000258216):​n.360-32878C>T 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 0.0857 in 152,132 control chromosomes in the GnomAD database, including 798 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 0.086 (798 hom., cov: 32)
• Consequence: ENST00000651272.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.486

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.164 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107984543	XR_007063399.1	n.171-32878C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000651272.1	n.360-32878C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0857 AC: 13033 AN: 152014 Hom.: 795 Cov.: 32

Gnomad AFR AF: 0.0349

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.0386

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.0721

Gnomad FIN AF: 0.174

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0843

Gnomad OTH AF: 0.0795

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

GnomAD4 genome AF: 0.0857 AC: 13042 AN: 152132 Hom.: 798 Cov.: 32 AF XY: 0.0925 AC XY: 6878 AN XY: 74356

Gnomad4 AFR AF: 0.0350

Gnomad4 AMR AF: 0.169

Gnomad4 ASJ AF: 0.0386

Gnomad4 EAS AF: 0.145

Gnomad4 SAS AF: 0.0720

Gnomad4 FIN AF: 0.174

Gnomad4 NFE AF: 0.0843

Gnomad4 OTH AF: 0.0787

Alfa AF: 0.0803 Hom.: 591

Bravo AF: 0.0861

Asia WGS AF: 0.0950 AC: 331 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.84
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12579003; hg19: chr12-90161860;