chr7-75471799-C-T

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.0931

Gnomad4 AMR AF: 0.516

Gnomad4 ASJ AF: 0.374

Gnomad4 EAS AF: 0.886

Gnomad4 SAS AF: 0.456

Gnomad4 FIN AF: 0.520

Gnomad4 NFE AF: 0.411

Gnomad4 OTH AF: 0.379

Alfa AF: 0.379 Hom.: 5389

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
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

Publications

LitVar

Other links and lift over

dbSNP: rs17207196; hg19: chr7-75101065;