rs536195330

Variant names:

• chr1-979313-C-A
• NM_001394713.1:c.1717G>T

Your query was ambiguous. Multiple possible variants found:

• chr1-979313-C-A
• chr1-979313-C-G
• chr1-979313-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001394713.1(PERM1):​c.1717G>T​(p.Gly573Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000173 in 1,384,630 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 10/16 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G573R) has been classified as Likely benign.

• Frequency:
  • Genomes: not found (cov: 34)
  • Exomes 𝑓: 0.000017 (0 hom.)
• Consequence: PERM1 NM_001394713.1 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40

Genes affected

PERM1 (HGNC:28208): (PPARGC1 and ESRR induced regulator, muscle 1) Involved in response to muscle activity. Predicted to be active in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.19049293).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PERM1	NM_001394713.1	c.1717G>T	p.Gly573Trp	missense_variant	Exon 2 of 4	ENST00000433179.4	NP_001381642.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PERM1	ENST00000433179.4	c.1717G>T	p.Gly573Trp	missense_variant	Exon 2 of 4	5	NM_001394713.1	ENSP00000414022.3
PERM1	ENST00000694917.1	c.1717G>T	p.Gly573Trp	missense_variant	Exon 2 of 4			ENSP00000511592.1
PERM1	ENST00000341290.6	c.1375G>T	p.Gly459Trp	missense_variant	Exon 3 of 5	2		ENSP00000343864.2

Frequencies

GnomAD3 genomes Cov.: 34

GnomAD4 exome AF: 0.0000173 AC: 24 AN: 1384630 Hom.: 0 Cov.: 79 AF XY: 0.0000161 AC XY: 11 AN XY: 681248

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000215

Gnomad4 OTH exome AF: 0.0000174

GnomAD4 genome Cov.: 34

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.29
BayesDel_addAF	Benign	-0.14	T
BayesDel_noAF	Benign	-0.44
CADD	Benign	15
DANN	Uncertain	0.99
DEOGEN2	Benign	0.11	.;T
Eigen	Benign	-0.52
Eigen_PC	Benign	-0.75
FATHMM_MKL	Benign	0.070	N
LIST_S2	Benign	0.51	T;T
M_CAP	Uncertain	0.095	D
MetaRNN	Benign	0.19	T;T
MetaSVM	Benign	-0.87	T
PROVEAN	Uncertain	-3.7	D;.
REVEL	Benign	0.053
Sift	Uncertain	0.010	D;.
Sift4G	Uncertain	0.030	D;D
Vest4		0.24
MVP		0.25
ClinPred		0.84	D
GERP RS		-0.52
Varity_R		0.029
gMVP		0.082

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr1-914693;