rs599839

Variant names:

• chr1-109279544-G-A
• rs599839
• NM_001032291.3:c.*609C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-109279544-G-A
• chr1-109279544-G-C
• chr1-109279544-G-T

Variant summary

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

The NM_001032291.3(PSRC1):​c.*609C>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.638 in 152,288 control chromosomes in the GnomAD database, including 35,004 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 0.64 (34921 hom., cov: 32)
  • Exomes 𝑓: 0.81 (83 hom.)
• Consequence: PSRC1 NM_001032291.3 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.902
• Publications: 318 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.901 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PSRC1	NM_001032291.3	c.*609C>T		downstream_gene_variant		ENST00000369909.7	NP_001027462.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PSRC1	ENST00000369909.7	c.*609C>T		downstream_gene_variant		1	NM_001032291.3	ENSP00000358925.2

Frequencies

GnomAD3 genomes AF: 0.638 AC: 96922 AN: 151912 Hom.: 34921 Cov.: 32

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.658

Gnomad AMR AF: 0.737

Gnomad ASJ AF: 0.828

Gnomad EAS AF: 0.922

Gnomad SAS AF: 0.746

Gnomad FIN AF: 0.775

Gnomad MID AF: 0.850

Gnomad NFE AF: 0.772

Gnomad OTH AF: 0.685

GnomAD4 exome AF: 0.810 AC: 209 AN: 258 Hom.: 83 Cov.: 0 AF XY: 0.808 AC XY: 118 AN XY: 146

African (AFR) AC: 0 AN: 0

American (AMR) AF: 0.500 AC: 3 AN: 6

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 1.00 AC: 2 AN: 2

European-Finnish (FIN) AF: 0.809 AC: 157 AN: 194

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.833 AC: 45 AN: 54

Other (OTH) AF: 1.00 AC: 2 AN: 2

GnomAD4 genome AF: 0.638 AC: 96942 AN: 152030 Hom.: 34921 Cov.: 32 AF XY: 0.641 AC XY: 47669 AN XY: 74326

African (AFR) AF: 0.276 AC: 11448 AN: 41414

American (AMR) AF: 0.737 AC: 11252 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.828 AC: 2867 AN: 3464

East Asian (EAS) AF: 0.922 AC: 4782 AN: 5184

South Asian (SAS) AF: 0.747 AC: 3599 AN: 4820

European-Finnish (FIN) AF: 0.775 AC: 8203 AN: 10580

Middle Eastern (MID) AF: 0.842 AC: 246 AN: 292

European-Non Finnish (NFE) AF: 0.772 AC: 52491 AN: 67984

Other (OTH) AF: 0.688 AC: 1454 AN: 2114

Alfa AF: 0.731 Hom.: 159910

Bravo AF: 0.618

Asia WGS AF: 0.790 AC: 2749 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.0
DANN	Benign	0.81
PhyloP100		-0.90

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs599839; hg19: chr1-109822166;