4-75008063-C-G

Variant names:

• chr4-75008063-C-G
• rs9307434
• NM_015393.4:c.44-4362C>G

Variant summary

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

The NM_015393.4(PARM1):​c.44-4362C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.313 in 152,152 control chromosomes in the GnomAD database, including 9,588 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 0.31 (9588 hom., cov: 33)
• Consequence: PARM1 NM_015393.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.689
• Publications: 1 publications found

Genes affected

PARM1 (HGNC:24536): (prostate androgen-regulated mucin-like protein 1) Predicted to be involved in positive regulation of telomerase activity. Located in several cellular components, including Golgi apparatus; endosome; and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000248165 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.566 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PARM1	NM_015393.4	c.44-4362C>G		intron_variant	Intron 1 of 3	ENST00000307428.7	NP_056208.2
PARM1	XM_011531833.1	c.149-4362C>G		intron_variant	Intron 2 of 4		XP_011530135.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PARM1	ENST00000307428.7	c.44-4362C>G		intron_variant	Intron 1 of 3	1	NM_015393.4	ENSP00000370224.3
PARM1	ENST00000513238.5	c.44-25820C>G		intron_variant	Intron 1 of 2	3		ENSP00000424276.1
ENSG00000248165	ENST00000513770.1	n.52-8892G>C		intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes AF: 0.313 AC: 47585 AN: 152034 Hom.: 9549 Cov.: 33

Gnomad AFR AF: 0.571

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.343

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.313 AC: 47687 AN: 152152 Hom.: 9588 Cov.: 33 AF XY: 0.313 AC XY: 23258 AN XY: 74368

African (AFR) AF: 0.572 AC: 23722 AN: 41478

American (AMR) AF: 0.299 AC: 4566 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.235 AC: 817 AN: 3472

East Asian (EAS) AF: 0.343 AC: 1780 AN: 5186

South Asian (SAS) AF: 0.196 AC: 945 AN: 4826

European-Finnish (FIN) AF: 0.180 AC: 1907 AN: 10592

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.191 AC: 12990 AN: 67986

Other (OTH) AF: 0.306 AC: 647 AN: 2114

Alfa AF: 0.0999 Hom.: 130

Bravo AF: 0.338

Asia WGS AF: 0.299 AC: 1039 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.72
DANN	Benign	0.64
PhyloP100		-0.69
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs9307434; hg19: chr4-75933273;