4-75008063-C-G

Position:

• chr4-75008063-C-G

Variant summary

Our verdict is Benign. Variant got -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

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
PARM1	NM_015393.4	c.44-4362C>G		intron_variant		ENST00000307428.7
PARM1	XM_011531833.1	c.149-4362C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PARM1	ENST00000307428.7	c.44-4362C>G		intron_variant		1	NM_015393.4	P1
	ENST00000513770.1	n.52-8892G>C		intron_variant, non_coding_transcript_variant		3
PARM1	ENST00000513238.5	c.44-25820C>G		intron_variant		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

Gnomad4 AFR AF: 0.572

Gnomad4 AMR AF: 0.299

Gnomad4 ASJ AF: 0.235

Gnomad4 EAS AF: 0.343

Gnomad4 SAS AF: 0.196

Gnomad4 FIN AF: 0.180

Gnomad4 NFE AF: 0.191

Gnomad4 OTH AF: 0.306

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs9307434; hg19: chr4-75933273;