rs14000

chr1-109279887-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001032291.3(PSRC1):c.*266A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0999 in 541,084 control chromosomes in the GnomAD database, including 3,294 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 0.12 (1213 hom., cov: 32)
  • Exomes 𝑓: 0.093 (2081 hom.)
• Consequence: PSRC1 NM_001032291.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00100

Genes affected

PSRC1 (HGNC:24472): (proline and serine rich coiled-coil 1) This gene encodes a proline-rich protein that is a target for regulation by the tumor suppressor protein p53. The encoded protein plays an important role in mitosis by recruiting and regulating microtubule depolymerases that destabalize microtubules. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Apr 2014]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.165 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PSRC1	NM_001032291.3	c.*266A>G		3_prime_UTR_variant	8/8	ENST00000369909.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PSRC1	ENST00000369909.7	c.*266A>G		3_prime_UTR_variant	8/8	1	NM_001032291.3	P2

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17955 AN: 151962 Hom.: 1216 Cov.: 32

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.0881

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.000963

Gnomad SAS AF: 0.0213

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.114

GnomAD4 exome AF: 0.0928 AC: 36108 AN: 389004 Hom.: 2081 Cov.: 3 AF XY: 0.0900 AC XY: 18277 AN XY: 203184

Gnomad4 AFR exome AF: 0.169

Gnomad4 AMR exome AF: 0.0704

Gnomad4 ASJ exome AF: 0.130

Gnomad4 EAS exome AF: 0.000502

Gnomad4 SAS exome AF: 0.0270

Gnomad4 FIN exome AF: 0.113

Gnomad4 NFE exome AF: 0.107

Gnomad4 OTH exome AF: 0.100

GnomAD4 genome AF: 0.118 AC: 17963 AN: 152080 Hom.: 1213 Cov.: 32 AF XY: 0.116 AC XY: 8611 AN XY: 74358

Gnomad4 AFR AF: 0.168

Gnomad4 AMR AF: 0.0879

Gnomad4 ASJ AF: 0.139

Gnomad4 EAS AF: 0.000966

Gnomad4 SAS AF: 0.0211

Gnomad4 FIN AF: 0.124

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.113

Alfa AF: 0.107 Hom.: 1397

Bravo AF: 0.118

Asia WGS AF: 0.0270 AC: 95 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	10
Dann	Benign	0.75

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs14000; hg19: chr1-109822509;