rs9366689

Variant names:

• chr6-27308392-C-A
• rs9366689
• NM_033482.4:c.*671G>T

Your query was ambiguous. Multiple possible variants found:

• chr6-27308392-C-A
• chr6-27308392-C-G

Variant summary

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

The NM_033482.4(POM121L2):​c.*671G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.452 in 151,514 control chromosomes in the GnomAD database, including 16,512 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 0.45 (16512 hom., cov: 33)
• Consequence: POM121L2 NM_033482.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.339
• Publications: 6 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.606 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
POM121L2	NM_033482.4	c.*671G>T		3_prime_UTR_variant	Exon 1 of 1	ENST00000444565.2	NP_258443.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
POM121L2	ENST00000444565.2	c.*671G>T		3_prime_UTR_variant	Exon 1 of 1	6	NM_033482.4	ENSP00000392726.1
POM121L2	ENST00000429945.1	c.216+2705G>T		intron_variant	Intron 1 of 1	3		ENSP00000415181.1

Frequencies

GnomAD3 genomes AF: 0.452 AC: 68387 AN: 151398 Hom.: 16500 Cov.: 33

Gnomad AFR AF: 0.613

Gnomad AMI AF: 0.544

Gnomad AMR AF: 0.381

Gnomad ASJ AF: 0.448

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.384

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.417

Gnomad OTH AF: 0.478

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

GnomAD4 genome AF: 0.452 AC: 68433 AN: 151514 Hom.: 16512 Cov.: 33 AF XY: 0.445 AC XY: 32965 AN XY: 74026

African (AFR) AF: 0.613 AC: 25139 AN: 41022

American (AMR) AF: 0.380 AC: 5790 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.448 AC: 1554 AN: 3468

East Asian (EAS) AF: 0.180 AC: 928 AN: 5144

South Asian (SAS) AF: 0.384 AC: 1849 AN: 4816

European-Finnish (FIN) AF: 0.303 AC: 3196 AN: 10554

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.417 AC: 28329 AN: 67958

Other (OTH) AF: 0.473 AC: 997 AN: 2110

Alfa AF: 0.433 Hom.: 4026

Bravo AF: 0.464

Asia WGS AF: 0.277 AC: 963 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.50
DANN	Benign	0.49
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs9366689; hg19: chr6-27276171;