chr5-75701931-T-C

Position:

• chr5-75701931-T-C

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
POC5	NM_001099271.2	c.513+674A>G		intron_variant		ENST00000428202.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
POC5	ENST00000428202.7	c.513+674A>G		intron_variant		1	NM_001099271.2	P1

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

Gnomad4 AFR AF: 0.501

Gnomad4 AMR AF: 0.392

Gnomad4 ASJ AF: 0.414

Gnomad4 EAS AF: 0.527

Gnomad4 SAS AF: 0.559

Gnomad4 FIN AF: 0.388

Gnomad4 NFE AF: 0.366

Gnomad4 OTH AF: 0.380

Alfa AF: 0.373 Hom.: 17857

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

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: rs10057967; hg19: chr5-74997756;