rs566393302

Variant names:

• chr1-981131-C-G
• rs566393302
• NM_001394713.1:c.-102G>C

Your query was ambiguous. Multiple possible variants found:

• chr1-981131-C-G
• chr1-981131-C-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001394713.1(PERM1):​c.-102G>C variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000716 in 1,396,846 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 34)
  • Exomes 𝑓: 7.2e-7 (0 hom.)
• Consequence: PERM1 NM_001394713.1 5_prime_UTR_premature_start_codon_gain
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.920

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 Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PERM1	NM_001394713.1	c.-102G>C		5_prime_UTR_premature_start_codon_gain_variant	Exon 2 of 4	ENST00000433179.4	NP_001381642.1
PERM1	NM_001394713.1	c.-102G>C		5_prime_UTR_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.-102G>C		5_prime_UTR_premature_start_codon_gain_variant	Exon 2 of 4	5	NM_001394713.1	ENSP00000414022.3
PERM1	ENST00000433179.4	c.-102G>C		5_prime_UTR_variant	Exon 2 of 4	5	NM_001394713.1	ENSP00000414022.3
PERM1	ENST00000694917.1	c.-18-84G>C		intron_variant	Intron 1 of 3			ENSP00000511592.1
PERM1	ENST00000341290.6	c.30+6G>C		splice_region_variant, intron_variant	Intron 2 of 4	2		ENSP00000343864.2

Frequencies

GnomAD3 genomes Cov.: 34

GnomAD4 exome AF: 7.16e-7 AC: 1 AN: 1396846 Hom.: 0 Cov.: 41 AF XY: 0.00 AC XY: 0 AN XY: 688858

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: 9.27e-7

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 34

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.6
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs566393302; hg19: chr1-916511;