rs7136572

Variant names:

• chr12-95566012-A-G
• rs7136572
• ENST00000626376.2:n.219+14212A>G

Variant summary

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

The ENST00000626376.2(PGAM1P5):​n.219+14212A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0716 in 152,204 control chromosomes in the GnomAD database, including 925 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 0.072 (925 hom., cov: 32)
• Consequence: PGAM1P5 ENST00000626376.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.526
• Publications: 9 publications found

Genes affected

PGAM1P5 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.324 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
PGAM1P5	ENST00000626376.2	n.219+14212A>G		intron_variant	Intron 1 of 1	5

Frequencies

GnomAD3 genomes AF: 0.0715 AC: 10881 AN: 152086 Hom.: 923 Cov.: 32

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0453

Gnomad ASJ AF: 0.00720

Gnomad EAS AF: 0.338

Gnomad SAS AF: 0.0336

Gnomad FIN AF: 0.0490

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0128

Gnomad OTH AF: 0.0660

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

GnomAD4 genome AF: 0.0716 AC: 10897 AN: 152204 Hom.: 925 Cov.: 32 AF XY: 0.0735 AC XY: 5470 AN XY: 74426

African (AFR) AF: 0.162 AC: 6719 AN: 41516

American (AMR) AF: 0.0454 AC: 694 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.00720 AC: 25 AN: 3472

East Asian (EAS) AF: 0.337 AC: 1742 AN: 5168

South Asian (SAS) AF: 0.0330 AC: 159 AN: 4820

European-Finnish (FIN) AF: 0.0490 AC: 520 AN: 10606

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0128 AC: 873 AN: 68030

Other (OTH) AF: 0.0691 AC: 146 AN: 2114

Alfa AF: 0.0320 Hom.: 1170

Bravo AF: 0.0782

Asia WGS AF: 0.190 AC: 658 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.57
DANN	Benign	0.20
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs7136572; hg19: chr12-95959788;