7-75471799-C-T

Variant names:

• chr7-75471799-C-T
• rs17207196
• NM_001099415.3:c.-152+2905G>A

Variant summary

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

The NM_001099415.3(POM121C):​c.-152+2905G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.359 in 152,106 control chromosomes in the GnomAD database, including 12,606 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 0.36 (12606 hom., cov: 31)
• Consequence: POM121C NM_001099415.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.588
• Publications: 35 publications found

Genes affected

POM121C (HGNC:34005): (POM121 transmembrane nucleoporin C) 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 located in nuclear envelope. Predicted to be part of nuclear pore. [provided by Alliance of Genome Resources, Apr 2022]

POM121C Gene-Disease associations (from GenCC):

• schizophrenia

  Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.864 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
POM121C	NM_001099415.3	c.-152+2905G>A		intron_variant	Intron 3 of 14	ENST00000615331.5	NP_001092885.2
POM121C	NR_160303.1	n.864+2905G>A		intron_variant	Intron 4 of 4
POM121C	NR_160304.1	n.845+2905G>A		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
POM121C	ENST00000615331.5	c.-152+2905G>A		intron_variant	Intron 3 of 14	1	NM_001099415.3	ENSP00000481575.1
POM121C	ENST00000398379.2	c.-152+2905G>A		intron_variant	Intron 3 of 4	2		ENSP00000381415.2

Frequencies

GnomAD3 genomes AF: 0.359 AC: 54627 AN: 151988 Hom.: 12598 Cov.: 31

Gnomad AFR AF: 0.0931

Gnomad AMI AF: 0.546

Gnomad AMR AF: 0.515

Gnomad ASJ AF: 0.374

Gnomad EAS AF: 0.885

Gnomad SAS AF: 0.455

Gnomad FIN AF: 0.520

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.411

Gnomad OTH AF: 0.383

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

GnomAD4 genome AF: 0.359 AC: 54639 AN: 152106 Hom.: 12606 Cov.: 31 AF XY: 0.372 AC XY: 27632 AN XY: 74328

African (AFR) AF: 0.0931 AC: 3864 AN: 41508

American (AMR) AF: 0.516 AC: 7885 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.374 AC: 1298 AN: 3472

East Asian (EAS) AF: 0.886 AC: 4577 AN: 5168

South Asian (SAS) AF: 0.456 AC: 2199 AN: 4824

European-Finnish (FIN) AF: 0.520 AC: 5486 AN: 10560

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.411 AC: 27941 AN: 67990

Other (OTH) AF: 0.379 AC: 798 AN: 2108

Alfa AF: 0.393 Hom.: 8754

Bravo AF: 0.349

Asia WGS AF: 0.586 AC: 2034 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.9
DANN	Benign	0.79
PhyloP100		0.59
RBP_binding_hub_radar		0.77
RBP_regulation_power_radar		1.9

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs17207196; hg19: chr7-75101065;