rs9886448

Variant names:

• chr8-26512191-T-C
• rs9886448
• NM_007257.6:c.-619+1625A>G

Variant summary

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

The NM_007257.6(PNMA2):​c.-619+1625A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.156 in 152,210 control chromosomes in the GnomAD database, including 1,968 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 0.16 (1968 hom., cov: 33)
• Consequence: PNMA2 NM_007257.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• Publications: 2 publications found

Genes affected

PNMA2 (HGNC:9159): (PNMA family member 2) Predicted to be involved in positive regulation of apoptotic process. Predicted to be located in nucleolus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.209 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_007257.6. 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
	PNMA2	NM_007257.6	MANE Select	c.-619+1625A>G		intron	N/A	NP_009188.1	Q9UL42

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PNMA2	ENST00000522362.7	TSL:1 MANE Select	c.-619+1625A>G		intron	N/A	ENSP00000429344.1	Q9UL42
	PNMA2	ENST00000854209.1		c.-736-425A>G		intron	N/A	ENSP00000524268.1
	PNMA2	ENST00000939502.1		c.-617+1625A>G		intron	N/A	ENSP00000609561.1

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23721 AN: 152092 Hom.: 1951 Cov.: 33

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.0844

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.169

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.140

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

GnomAD4 genome AF: 0.156 AC: 23773 AN: 152210 Hom.: 1968 Cov.: 33 AF XY: 0.161 AC XY: 11973 AN XY: 74406

African (AFR) AF: 0.193 AC: 8012 AN: 41524

American (AMR) AF: 0.194 AC: 2974 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.146 AC: 507 AN: 3470

East Asian (EAS) AF: 0.219 AC: 1134 AN: 5168

South Asian (SAS) AF: 0.205 AC: 985 AN: 4816

European-Finnish (FIN) AF: 0.169 AC: 1794 AN: 10594

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.117 AC: 7966 AN: 68014

Other (OTH) AF: 0.141 AC: 299 AN: 2116

Alfa AF: 0.130 Hom.: 1927

Bravo AF: 0.160

Asia WGS AF: 0.215 AC: 748 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.2
DANN	Benign	0.71
PhyloP100		-1.4
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs9886448; hg19: chr8-26369707;