12-132117051-A-G

Variant names:

• chr12-132117051-A-G
• rs12422267
• ENST00000332441.7:n.1661+2506A>G

Variant summary

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

The ENST00000332441.7(ENSG00000291171):​n.1661+2506A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0627 in 152,278 control chromosomes in the GnomAD database, including 411 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 0.063 (411 hom., cov: 33)
• Consequence: ENSG00000291171 ENST00000332441.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.294
• Publications: 8 publications found

Genes affected

ENSG00000291171 (HGNC:):

EP400P1 (HGNC:26602): (EP400 pseudogene 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0919 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EP400P1	NR_003290.2	n.471+2506A>G		intron_variant	Intron 5 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000291171	ENST00000332441.7	n.1661+2506A>G		intron_variant	Intron 6 of 10	2
ENSG00000291171	ENST00000446190.5	n.1719+2506A>G		intron_variant	Intron 5 of 7	2
ENSG00000291171	ENST00000488030.5	n.441+2506A>G		intron_variant	Intron 5 of 9	2

Frequencies

GnomAD3 genomes AF: 0.0627 AC: 9534 AN: 152160 Hom.: 410 Cov.: 33

Gnomad AFR AF: 0.0174

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.0529

Gnomad ASJ AF: 0.0562

Gnomad EAS AF: 0.0102

Gnomad SAS AF: 0.0340

Gnomad FIN AF: 0.0905

Gnomad MID AF: 0.0573

Gnomad NFE AF: 0.0939

Gnomad OTH AF: 0.0517

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

GnomAD4 genome AF: 0.0627 AC: 9541 AN: 152278 Hom.: 411 Cov.: 33 AF XY: 0.0609 AC XY: 4538 AN XY: 74470

African (AFR) AF: 0.0172 AC: 717 AN: 41570

American (AMR) AF: 0.0529 AC: 809 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0562 AC: 195 AN: 3470

East Asian (EAS) AF: 0.0102 AC: 53 AN: 5180

South Asian (SAS) AF: 0.0336 AC: 162 AN: 4826

European-Finnish (FIN) AF: 0.0905 AC: 961 AN: 10618

Middle Eastern (MID) AF: 0.0616 AC: 18 AN: 292

European-Non Finnish (NFE) AF: 0.0939 AC: 6383 AN: 67996

Other (OTH) AF: 0.0563 AC: 119 AN: 2112

Alfa AF: 0.0807 Hom.: 1069

Bravo AF: 0.0584

Asia WGS AF: 0.0330 AC: 115 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.5
DANN	Benign	0.74
PhyloP100		0.29
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs12422267; hg19: chr12-132601596;