12-96432392-C-A

Position:

• chr12-96432392-C-A

Variant summary

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

The ENST00000548740.1(ENSG00000258272):​n.227-2925G>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 0.47 in 151,724 control chromosomes in the GnomAD database, including 17,147 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 0.47 (17147 hom., cov: 30)
• Consequence: ENST00000548740.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.205

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.528 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
	ENST00000548740.1	n.227-2925G>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.470 AC: 71226 AN: 151604 Hom.: 17145 Cov.: 30

Gnomad AFR AF: 0.360

Gnomad AMI AF: 0.529

Gnomad AMR AF: 0.488

Gnomad ASJ AF: 0.551

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.396

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.533

Gnomad OTH AF: 0.487

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

GnomAD4 genome AF: 0.470 AC: 71239 AN: 151724 Hom.: 17147 Cov.: 30 AF XY: 0.466 AC XY: 34524 AN XY: 74104

Gnomad4 AFR AF: 0.359

Gnomad4 AMR AF: 0.488

Gnomad4 ASJ AF: 0.551

Gnomad4 EAS AF: 0.424

Gnomad4 SAS AF: 0.396

Gnomad4 FIN AF: 0.485

Gnomad4 NFE AF: 0.533

Gnomad4 OTH AF: 0.490

Alfa AF: 0.524 Hom.: 42198

Bravo AF: 0.463

Asia WGS AF: 0.411 AC: 1430 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.94
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7312607; hg19: chr12-96826170;