rs4826957

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000372451.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYCLP1	ENST00000372451.2	TSL:6	n.314G>C		non_coding_transcript_exon	Exon 1 of 1

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4826957;

hg19: chrX-106516125;