rs14000

Variant names:

• chr1-109279887-T-C
• rs14000
• NM_001032291.3:c.*266A>G

Your query was ambiguous. Multiple possible variants found:

• chr1-109279887-T-C
• chr1-109279887-T-G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 19 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001032291.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PSRC1	NM_001032291.3	MANE Select	c.*266A>G		3_prime_UTR	Exon 8 of 8	NP_001027462.1	Q6PGN9-2
	PSRC1	NM_001363309.2		c.*266A>G		3_prime_UTR	Exon 7 of 7	NP_001350238.1	Q6PGN9-1
	PSRC1	NM_001394005.1		c.*266A>G		3_prime_UTR	Exon 7 of 7	NP_001380934.1	Q6PGN9-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PSRC1	ENST00000369909.7	TSL:1 MANE Select	c.*266A>G		3_prime_UTR	Exon 8 of 8	ENSP00000358925.2	Q6PGN9-2
	PSRC1	ENST00000369907.7	TSL:1	c.*266A>G		3_prime_UTR	Exon 8 of 8	ENSP00000358923.3	Q6PGN9-2
	PSRC1	ENST00000369904.7	TSL:1	c.*234A>G		3_prime_UTR	Exon 8 of 8	ENSP00000358920.3	Q6PGN9-3

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

African (AFR) AF: 0.169 AC: 2001 AN: 11822

American (AMR) AF: 0.0704 AC: 1228 AN: 17452

Ashkenazi Jewish (ASJ) AF: 0.130 AC: 1554 AN: 11912

East Asian (EAS) AF: 0.000502 AC: 15 AN: 29876

South Asian (SAS) AF: 0.0270 AC: 877 AN: 32536

European-Finnish (FIN) AF: 0.113 AC: 3245 AN: 28796

Middle Eastern (MID) AF: 0.103 AC: 175 AN: 1706

European-Non Finnish (NFE) AF: 0.107 AC: 24710 AN: 231926

Other (OTH) AF: 0.100 AC: 2303 AN: 22978

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

African (AFR) AF: 0.168 AC: 6987 AN: 41522

American (AMR) AF: 0.0879 AC: 1345 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.139 AC: 462 AN: 3314

East Asian (EAS) AF: 0.000966 AC: 5 AN: 5178

South Asian (SAS) AF: 0.0211 AC: 102 AN: 4824

European-Finnish (FIN) AF: 0.124 AC: 1313 AN: 10602

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.107 AC: 7293 AN: 68014

Other (OTH) AF: 0.113 AC: 239 AN: 2114

Alfa AF: 0.107 Hom.: 1812

Bravo AF: 0.118

Asia WGS AF: 0.0270 AC: 95 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	10
DANN	Benign	0.75
PhyloP100		0.0010
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs14000; hg19: chr1-109822509;