rs4826957

chrX-107272895-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000372451.2(MYCLP1):n.314G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.255 in 266,450 control chromosomes in the GnomAD database, including 7,600 homozygotes. There are 20,834 hemizygotes in GnomAD. 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 0.28 (3831 hom., 8918 hem., cov: 23)
  • Exomes 𝑓: 0.24 (3769 hom. 11916 hem.)
• Consequence: MYCLP1 ENST00000372451.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.315

Genes affected

MYCLP1 (HGNC:7556): (MYCL pseudogene 1) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.546 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYCLP1	ENST00000372451.2	n.314G>C		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.279 AC: 30843 AN: 110452 Hom.: 3839 Cov.: 23 AF XY: 0.272 AC XY: 8889 AN XY: 32740

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.431

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.567

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.322

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.306

GnomAD4 exome AF: 0.237 AC: 36959 AN: 155945 Hom.: 3769 Cov.: 0 AF XY: 0.258 AC XY: 11916 AN XY: 46229

Gnomad4 AFR exome AF: 0.437

Gnomad4 AMR exome AF: 0.501

Gnomad4 ASJ exome AF: 0.305

Gnomad4 EAS exome AF: 0.611

Gnomad4 SAS exome AF: 0.312

Gnomad4 FIN exome AF: 0.129

Gnomad4 NFE exome AF: 0.175

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.279 AC: 30855 AN: 110505 Hom.: 3831 Cov.: 23 AF XY: 0.272 AC XY: 8918 AN XY: 32803

Gnomad4 AFR AF: 0.410

Gnomad4 AMR AF: 0.431

Gnomad4 ASJ AF: 0.302

Gnomad4 EAS AF: 0.567

Gnomad4 SAS AF: 0.306

Gnomad4 FIN AF: 0.115

Gnomad4 NFE AF: 0.172

Gnomad4 OTH AF: 0.301

Alfa AF: 0.218 Hom.: 1339

Bravo AF: 0.319

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
Cadd	Benign	6.7
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4826957; hg19: chrX-106516125;