5-75701931-T-C

Variant names:

• chr5-75701931-T-C
• rs10057967
• NM_001099271.2:c.513+674A>G

Variant summary

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

The NM_001099271.2(POC5):​c.513+674A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.42 in 151,946 control chromosomes in the GnomAD database, including 13,750 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 0.42 (13750 hom., cov: 31)
• Consequence: POC5 NM_001099271.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.329
• Publications: 25 publications found

Genes affected

POC5 (HGNC:26658): (POC5 centriolar protein) Predicted to enable identical protein binding activity. Located in centrosome; cytosol; and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

POC5 Gene-Disease associations (from GenCC):

• retinitis pigmentosa

  Inheritance: AR Classification: LIMITED Submitted by: Franklin by Genoox

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.542 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
POC5	NM_001099271.2	c.513+674A>G		intron_variant	Intron 5 of 11	ENST00000428202.7	NP_001092741.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
POC5	ENST00000428202.7	c.513+674A>G		intron_variant	Intron 5 of 11	1	NM_001099271.2	ENSP00000410216.2

Frequencies

GnomAD3 genomes AF: 0.420 AC: 63776 AN: 151828 Hom.: 13738 Cov.: 31

Gnomad AFR AF: 0.502

Gnomad AMI AF: 0.445

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.414

Gnomad EAS AF: 0.527

Gnomad SAS AF: 0.560

Gnomad FIN AF: 0.388

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.366

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.420 AC: 63827 AN: 151946 Hom.: 13750 Cov.: 31 AF XY: 0.425 AC XY: 31583 AN XY: 74268

African (AFR) AF: 0.501 AC: 20770 AN: 41434

American (AMR) AF: 0.392 AC: 5996 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.414 AC: 1435 AN: 3470

East Asian (EAS) AF: 0.527 AC: 2714 AN: 5152

South Asian (SAS) AF: 0.559 AC: 2699 AN: 4824

European-Finnish (FIN) AF: 0.388 AC: 4090 AN: 10540

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.366 AC: 24830 AN: 67932

Other (OTH) AF: 0.380 AC: 800 AN: 2108

Alfa AF: 0.383 Hom.: 30726

Bravo AF: 0.418

Asia WGS AF: 0.545 AC: 1893 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	6.6
DANN	Benign	0.61
PhyloP100		-0.33
Mutation Taster		=100/0	polymorphism (auto)

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: rs10057967; hg19: chr5-74997756;