rs20508

Variant names:

• chr12-97688809-G-A
• rs20508
• ENST00000701071.2:n.321-44202C>T

Variant summary

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

The ENST00000701071.2(PAFAH1B2P2):​n.321-44202C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.759 in 152,130 control chromosomes in the GnomAD database, including 44,170 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 0.76 (44170 hom., cov: 33)
• Consequence: PAFAH1B2P2 ENST00000701071.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.959
• Publications: 5 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 = 0.851 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000701071.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PAFAH1B2P2	ENST00000701071.2		n.321-44202C>T		intron	N/A
	PAFAH1B2P2	ENST00000847471.1		n.316+24895C>T		intron	N/A
	PAFAH1B2P2	ENST00000847472.1		n.410+30375C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.759 AC: 115360 AN: 152012 Hom.: 44123 Cov.: 33

Gnomad AFR AF: 0.858

Gnomad AMI AF: 0.817

Gnomad AMR AF: 0.796

Gnomad ASJ AF: 0.793

Gnomad EAS AF: 0.590

Gnomad SAS AF: 0.641

Gnomad FIN AF: 0.691

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.719

Gnomad OTH AF: 0.773

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

GnomAD4 genome AF: 0.759 AC: 115466 AN: 152130 Hom.: 44170 Cov.: 33 AF XY: 0.754 AC XY: 56034 AN XY: 74360

African (AFR) AF: 0.858 AC: 35633 AN: 41524

American (AMR) AF: 0.797 AC: 12165 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.793 AC: 2752 AN: 3472

East Asian (EAS) AF: 0.590 AC: 3051 AN: 5172

South Asian (SAS) AF: 0.642 AC: 3099 AN: 4824

European-Finnish (FIN) AF: 0.691 AC: 7299 AN: 10564

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

European-Non Finnish (NFE) AF: 0.719 AC: 48847 AN: 67982

Other (OTH) AF: 0.771 AC: 1629 AN: 2114

Alfa AF: 0.730 Hom.: 20832

Bravo AF: 0.775

Asia WGS AF: 0.630 AC: 2193 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	2.8
DANN	Benign	0.26
PhyloP100		0.96

Splicing

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

Other links and lift over

dbSNP: rs20508; hg19: chr12-98082587;