chr1-52598362-G-A

Variant names:

• chr1-52598362-G-A
• rs835342
• ENST00000807137.1:n.129-387G>A

Variant summary

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

The ENST00000807137.1(ENSG00000272371):​n.129-387G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.535 in 151,706 control chromosomes in the GnomAD database, including 21,997 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 0.53 (21997 hom., cov: 31)
• Consequence: ENSG00000272371 ENST00000807137.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.212
• Publications: 34 publications found

Genes affected

ENSG00000272371 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.746 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000807137.1. 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
	ENSG00000272371	ENST00000807137.1		n.129-387G>A		intron	N/A
	ENSG00000272371	ENST00000807138.1		n.51-387G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.535 AC: 81122 AN: 151588 Hom.: 21987 Cov.: 31

Gnomad AFR AF: 0.437

Gnomad AMI AF: 0.433

Gnomad AMR AF: 0.632

Gnomad ASJ AF: 0.613

Gnomad EAS AF: 0.766

Gnomad SAS AF: 0.630

Gnomad FIN AF: 0.563

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.540

Gnomad OTH AF: 0.566

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

GnomAD4 genome AF: 0.535 AC: 81155 AN: 151706 Hom.: 21997 Cov.: 31 AF XY: 0.541 AC XY: 40068 AN XY: 74108

African (AFR) AF: 0.437 AC: 18049 AN: 41312

American (AMR) AF: 0.632 AC: 9627 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.613 AC: 2130 AN: 3472

East Asian (EAS) AF: 0.766 AC: 3958 AN: 5166

South Asian (SAS) AF: 0.629 AC: 3026 AN: 4808

European-Finnish (FIN) AF: 0.563 AC: 5905 AN: 10482

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.540 AC: 36677 AN: 67910

Other (OTH) AF: 0.568 AC: 1198 AN: 2110

Alfa AF: 0.542 Hom.: 102066

Bravo AF: 0.538

Asia WGS AF: 0.719 AC: 2498 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.3
DANN	Benign	0.79
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs835342; hg19: chr1-53064034;