ENST00000372451.2:n.314G>C

Variant names:

• chrX-107272895-G-C
• rs4826957
• ENST00000372451.2:n.314G>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
MYCLP1		n.107272895G>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYCLP1	ENST00000372451.2	n.314G>C		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.279 AC: 30843 AN: 110452 Hom.: 3839 Cov.: 23

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

African (AFR) AF: 0.437 AC: 1770 AN: 4048

American (AMR) AF: 0.501 AC: 4062 AN: 8100

Ashkenazi Jewish (ASJ) AF: 0.305 AC: 1099 AN: 3598

East Asian (EAS) AF: 0.611 AC: 3924 AN: 6426

South Asian (SAS) AF: 0.312 AC: 6553 AN: 21020

European-Finnish (FIN) AF: 0.129 AC: 2345 AN: 18112

Middle Eastern (MID) AF: 0.315 AC: 223 AN: 708

European-Non Finnish (NFE) AF: 0.175 AC: 15040 AN: 86167

Other (OTH) AF: 0.250 AC: 1943 AN: 7766

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

African (AFR) AF: 0.410 AC: 12434 AN: 30344

American (AMR) AF: 0.431 AC: 4488 AN: 10407

Ashkenazi Jewish (ASJ) AF: 0.302 AC: 791 AN: 2622

East Asian (EAS) AF: 0.567 AC: 1931 AN: 3405

South Asian (SAS) AF: 0.306 AC: 784 AN: 2558

European-Finnish (FIN) AF: 0.115 AC: 687 AN: 5974

Middle Eastern (MID) AF: 0.302 AC: 64 AN: 212

European-Non Finnish (NFE) AF: 0.172 AC: 9078 AN: 52800

Other (OTH) AF: 0.301 AC: 454 AN: 1508

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
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs4826957; hg19: chrX-106516125;