1-109279386-G-T

Variant names:

• chr1-109279386-G-T
• rs4970837
• NM_001032291.3:c.*767C>A

Variant summary

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

The NM_001032291.3(PSRC1):​c.*767C>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.55 in 150,850 control chromosomes in the GnomAD database, including 26,513 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 0.55 (26513 hom., cov: 27)
• Consequence: PSRC1 NM_001032291.3 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365
• Publications: 13 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.91 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PSRC1	NM_001032291.3	MANE Select	c.*767C>A		downstream_gene	N/A	NP_001027462.1
	PSRC1	NM_001363309.2		c.*767C>A		downstream_gene	N/A	NP_001350238.1
	PSRC1	NM_001394005.1		c.*767C>A		downstream_gene	N/A	NP_001380934.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PSRC1	ENST00000369909.7	TSL:1 MANE Select	c.*767C>A		downstream_gene	N/A	ENSP00000358925.2
	PSRC1	ENST00000369907.7	TSL:1	c.*767C>A		downstream_gene	N/A	ENSP00000358923.3
	PSRC1	ENST00000369904.7	TSL:1	c.*735C>A		downstream_gene	N/A	ENSP00000358920.3

Frequencies

GnomAD3 genomes AF: 0.550 AC: 82880 AN: 150732 Hom.: 26504 Cov.: 27

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.660

Gnomad ASJ AF: 0.665

Gnomad EAS AF: 0.931

Gnomad SAS AF: 0.730

Gnomad FIN AF: 0.653

Gnomad MID AF: 0.784

Gnomad NFE AF: 0.668

Gnomad OTH AF: 0.592

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

GnomAD4 genome AF: 0.550 AC: 82903 AN: 150850 Hom.: 26513 Cov.: 27 AF XY: 0.554 AC XY: 40770 AN XY: 73616

African (AFR) AF: 0.206 AC: 8444 AN: 40944

American (AMR) AF: 0.660 AC: 10033 AN: 15194

Ashkenazi Jewish (ASJ) AF: 0.665 AC: 2302 AN: 3462

East Asian (EAS) AF: 0.932 AC: 4790 AN: 5140

South Asian (SAS) AF: 0.731 AC: 3488 AN: 4770

European-Finnish (FIN) AF: 0.653 AC: 6755 AN: 10338

Middle Eastern (MID) AF: 0.778 AC: 224 AN: 288

European-Non Finnish (NFE) AF: 0.668 AC: 45209 AN: 67718

Other (OTH) AF: 0.596 AC: 1245 AN: 2088

Alfa AF: 0.464 Hom.: 1505

Bravo AF: 0.533

Asia WGS AF: 0.791 AC: 2750 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.8
DANN	Benign	0.55
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs4970837; hg19: chr1-109822008;