ENST00000429945.1:c.217-7397G>A

Variant names:

• chr6-27293545-C-T
• rs7746199
• ENST00000429945.1:c.217-7397G>A

Variant summary

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

The ENST00000429945.1(POM121L2):​c.217-7397G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 151,822 control chromosomes in the GnomAD database, including 2,709 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 0.18 (2709 hom., cov: 31)
• Consequence: POM121L2 ENST00000429945.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.365
• Publications: 51 publications found

Genes affected

POM121L2 (HGNC:13973): (POM121 transmembrane nucleoporin like 2) Predicted to enable nuclear localization sequence binding activity. Predicted to be a structural constituent of nuclear pore. Predicted to be involved in RNA export from nucleus and protein import into nucleus. Predicted to be part of nuclear pore. [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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.241 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
POM121L2	ENST00000429945.1	c.217-7397G>A		intron_variant	Intron 1 of 1	3		ENSP00000415181.1

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26712 AN: 151704 Hom.: 2709 Cov.: 31

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.0249

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.0599

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.176 AC: 26724 AN: 151822 Hom.: 2709 Cov.: 31 AF XY: 0.169 AC XY: 12504 AN XY: 74182

African (AFR) AF: 0.245 AC: 10150 AN: 41354

American (AMR) AF: 0.156 AC: 2381 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.204 AC: 706 AN: 3466

East Asian (EAS) AF: 0.0248 AC: 128 AN: 5162

South Asian (SAS) AF: 0.118 AC: 566 AN: 4790

European-Finnish (FIN) AF: 0.0599 AC: 631 AN: 10528

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.169 AC: 11520 AN: 67972

Other (OTH) AF: 0.201 AC: 422 AN: 2100

Alfa AF: 0.173 Hom.: 10694

Bravo AF: 0.186

Asia WGS AF: 0.0850 AC: 297 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.77
DANN	Benign	0.74
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs7746199; hg19: chr6-27261324;