chr12-96432392-C-A

Variant names:

• chr12-96432392-C-A
• rs7312607
• ENST00000548740.1:n.227-2925G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000548740.1(ENSG00000258272):​n.227-2925G>T variant causes a intron 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: ENSG00000258272 ENST00000548740.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.205
• Publications: 4 publications found

Genes affected

ENSG00000258272 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000258272	ENST00000548740.1	n.227-2925G>T		intron_variant	Intron 2 of 3	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

African (AFR) AF: 0.359 AC: 14867 AN: 41364

American (AMR) AF: 0.488 AC: 7429 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.551 AC: 1910 AN: 3466

East Asian (EAS) AF: 0.424 AC: 2172 AN: 5124

South Asian (SAS) AF: 0.396 AC: 1904 AN: 4810

European-Finnish (FIN) AF: 0.485 AC: 5096 AN: 10504

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.533 AC: 36204 AN: 67916

Other (OTH) AF: 0.490 AC: 1029 AN: 2102

Alfa AF: 0.517 Hom.: 87237

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
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs7312607; hg19: chr12-96826170;