1-25908492-A-G

Variant names:

• chr1-25908492-A-G
• rs182455
• ENST00000722569.1:n.305A>G

Variant summary

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

The ENST00000722569.1(ENSG00000294297):​n.305A>G 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 0.585 in 151,690 control chromosomes in the GnomAD database, including 26,218 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 0.58 (26218 hom., cov: 30)
• Consequence: ENSG00000294297 ENST00000722569.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0140
• Publications: 20 publications found

Genes affected

ENSG00000294297 (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 (SAS) allele frequency at 95% confidence interval = 0.735 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000722569.1. 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
	ENSG00000294297	ENST00000722569.1		n.305A>G		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000294297	ENST00000722567.1		n.212+1224A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.585 AC: 88631 AN: 151574 Hom.: 26179 Cov.: 30

Gnomad AFR AF: 0.548

Gnomad AMI AF: 0.517

Gnomad AMR AF: 0.657

Gnomad ASJ AF: 0.469

Gnomad EAS AF: 0.669

Gnomad SAS AF: 0.755

Gnomad FIN AF: 0.523

Gnomad MID AF: 0.558

Gnomad NFE AF: 0.589

Gnomad OTH AF: 0.580

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

GnomAD4 genome AF: 0.585 AC: 88727 AN: 151690 Hom.: 26218 Cov.: 30 AF XY: 0.586 AC XY: 43412 AN XY: 74108

African (AFR) AF: 0.548 AC: 22642 AN: 41318

American (AMR) AF: 0.658 AC: 10020 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.469 AC: 1626 AN: 3466

East Asian (EAS) AF: 0.668 AC: 3460 AN: 5178

South Asian (SAS) AF: 0.755 AC: 3621 AN: 4794

European-Finnish (FIN) AF: 0.523 AC: 5472 AN: 10472

Middle Eastern (MID) AF: 0.569 AC: 165 AN: 290

European-Non Finnish (NFE) AF: 0.589 AC: 40032 AN: 67924

Other (OTH) AF: 0.579 AC: 1221 AN: 2108

Alfa AF: 0.590 Hom.: 8525

Bravo AF: 0.587

Asia WGS AF: 0.749 AC: 2605 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	4.9
DANN	Benign	0.52
PhyloP100		0.014

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: rs182455;

hg19: chr1-26234983;