chr12-97871686-G-A

Variant names:

• chr12-97871686-G-A
• rs10745813
• ENST00000847470.1:n.295+2354C>T

Variant summary

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

The ENST00000847470.1(PAFAH1B2P2):​n.295+2354C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.8 in 152,072 control chromosomes in the GnomAD database, including 49,320 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 0.80 (49320 hom., cov: 31)
• Consequence: PAFAH1B2P2 ENST00000847470.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.670
• Publications: 1 publications found

Genes affected

PAFAH1B2P2 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.871 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000847470.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PAFAH1B2P2	ENST00000847470.1		n.295+2354C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.799 AC: 121478 AN: 151954 Hom.: 49272 Cov.: 31

Gnomad AFR AF: 0.879

Gnomad AMI AF: 0.816

Gnomad AMR AF: 0.831

Gnomad ASJ AF: 0.826

Gnomad EAS AF: 0.477

Gnomad SAS AF: 0.611

Gnomad FIN AF: 0.649

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.803

Gnomad OTH AF: 0.822

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

GnomAD4 genome AF: 0.800 AC: 121585 AN: 152072 Hom.: 49320 Cov.: 31 AF XY: 0.789 AC XY: 58635 AN XY: 74310

African (AFR) AF: 0.879 AC: 36476 AN: 41502

American (AMR) AF: 0.831 AC: 12680 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.826 AC: 2863 AN: 3468

East Asian (EAS) AF: 0.478 AC: 2470 AN: 5164

South Asian (SAS) AF: 0.612 AC: 2946 AN: 4816

European-Finnish (FIN) AF: 0.649 AC: 6845 AN: 10546

Middle Eastern (MID) AF: 0.837 AC: 246 AN: 294

European-Non Finnish (NFE) AF: 0.803 AC: 54596 AN: 68000

Other (OTH) AF: 0.814 AC: 1720 AN: 2114

Alfa AF: 0.795 Hom.: 19353

Bravo AF: 0.819

Asia WGS AF: 0.528 AC: 1839 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.31
DANN	Benign	0.63
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs10745813; hg19: chr12-98265464;