rs3800316

Variant names:

• chr6-27288323-A-C
• rs3800316
• ENST00000429945.1:c.217-2175T>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000429945.1(POM121L2):​c.217-2175T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.321 in 152,156 control chromosomes in the GnomAD database, including 9,653 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 0.32 (9653 hom., cov: 32)
• Consequence: POM121L2 ENST00000429945.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.72

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

Verdict is Benign. Variant got -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 = 0.531 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.217-2175T>G		intron_variant	Intron 1 of 1	3		ENSP00000415181.1

Frequencies

GnomAD3 genomes AF: 0.321 AC: 48794 AN: 152038 Hom.: 9636 Cov.: 32

Gnomad AFR AF: 0.537

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.272

Gnomad EAS AF: 0.0328

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.347

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

GnomAD4 genome AF: 0.321 AC: 48834 AN: 152156 Hom.: 9653 Cov.: 32 AF XY: 0.309 AC XY: 22991 AN XY: 74386

Gnomad4 AFR AF: 0.537

Gnomad4 AMR AF: 0.276

Gnomad4 ASJ AF: 0.272

Gnomad4 EAS AF: 0.0329

Gnomad4 SAS AF: 0.196

Gnomad4 FIN AF: 0.110

Gnomad4 NFE AF: 0.265

Gnomad4 OTH AF: 0.344

Alfa AF: 0.290 Hom.: 6572

Bravo AF: 0.345

Asia WGS AF: 0.147 AC: 512 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.51
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3800316; hg19: chr6-27256102;