rs3800318

Variant names:

• chr6-27295862-A-T
• rs3800318
• ENST00000429945.1:c.217-9714T>A

Variant summary

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

The ENST00000429945.1(POM121L2):​c.217-9714T>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 152,088 control chromosomes in the GnomAD database, including 2,703 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 (2703 hom., cov: 32)
• Consequence: POM121L2 ENST00000429945.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0670

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=-0.83).
• 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.217-9714T>A		intron_variant	Intron 1 of 1	3		ENSP00000415181.1

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26729 AN: 151970 Hom.: 2703 Cov.: 32

Gnomad AFR AF: 0.245

Gnomad AMI AF: 0.175

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.0247

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.0594

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.170

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: 26741 AN: 152088 Hom.: 2703 Cov.: 32 AF XY: 0.168 AC XY: 12511 AN XY: 74382

Gnomad4 AFR AF: 0.245

Gnomad4 AMR AF: 0.156

Gnomad4 ASJ AF: 0.203

Gnomad4 EAS AF: 0.0245

Gnomad4 SAS AF: 0.118

Gnomad4 FIN AF: 0.0594

Gnomad4 NFE AF: 0.170

Gnomad4 OTH AF: 0.201

Alfa AF: 0.173 Hom.: 313

Bravo AF: 0.187

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	-0.83
CADD	Benign	2.5
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3800318; hg19: chr6-27263641;