1-155231444-G-A

Variant names:

• chr1-155231444-G-A
• rs1045253

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.389 in 151,940 control chromosomes in the GnomAD database, including 12,631 homozygotes. 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 0.39 (12631 hom., cov: 33)
• Consequence: MTX1LP intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.119
• Publications: 29 publications found

Genes affected

MTX1LP (HGNC:7505): (metaxin 1 pseudogene 1 [Source:HGNC Symbol%3BAcc:HGNC:7505])

ENSG00000302966 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.683 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000440904.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MTX1LP	ENST00000440904.1	TSL:6	n.115+223G>A		intron	N/A
	ENSG00000302966	ENST00000790740.1		n.154-1567G>A		intron	N/A
	ENSG00000302966	ENST00000790741.1		n.121-1309G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.388 AC: 58967 AN: 151822 Hom.: 12597 Cov.: 33

Gnomad AFR AF: 0.544

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.298

Gnomad EAS AF: 0.702

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.326

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.364

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.389 AC: 59044 AN: 151940 Hom.: 12631 Cov.: 33 AF XY: 0.388 AC XY: 28810 AN XY: 74252

African (AFR) AF: 0.544 AC: 22547 AN: 41414

American (AMR) AF: 0.351 AC: 5356 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.298 AC: 1034 AN: 3472

East Asian (EAS) AF: 0.702 AC: 3622 AN: 5162

South Asian (SAS) AF: 0.359 AC: 1730 AN: 4818

European-Finnish (FIN) AF: 0.326 AC: 3452 AN: 10574

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.299 AC: 20337 AN: 67934

Other (OTH) AF: 0.361 AC: 762 AN: 2108

Alfa AF: 0.313 Hom.: 10358

Bravo AF: 0.403

Asia WGS AF: 0.555 AC: 1930 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.41
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs1045253; hg19: chr1-155201235;