chr1-89100413-G-A

Variant names:

• chr1-89100413-G-A
• rs12725861
• ENST00000824610.1:n.425+1848G>A

Variant summary

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

The ENST00000824610.1(ENSG00000307222):​n.425+1848G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.398 in 151,770 control chromosomes in the GnomAD database, including 13,487 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 0.40 (13487 hom., cov: 29)
• Consequence: ENSG00000307222 ENST00000824610.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.229
• Publications: 5 publications found

Genes affected

ENSG00000307222 (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 (NFE) allele frequency at 95% confidence interval = 0.495 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000824610.1. 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
	ENSG00000307222	ENST00000824610.1		n.425+1848G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.398 AC: 60382 AN: 151652 Hom.: 13490 Cov.: 29

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.457

Gnomad AMR AF: 0.319

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.482

Gnomad FIN AF: 0.584

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.499

Gnomad OTH AF: 0.407

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

GnomAD4 genome AF: 0.398 AC: 60372 AN: 151770 Hom.: 13487 Cov.: 29 AF XY: 0.402 AC XY: 29831 AN XY: 74178

African (AFR) AF: 0.201 AC: 8316 AN: 41376

American (AMR) AF: 0.319 AC: 4865 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.411 AC: 1423 AN: 3460

East Asian (EAS) AF: 0.393 AC: 2026 AN: 5156

South Asian (SAS) AF: 0.483 AC: 2320 AN: 4802

European-Finnish (FIN) AF: 0.584 AC: 6140 AN: 10516

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.499 AC: 33878 AN: 67884

Other (OTH) AF: 0.405 AC: 855 AN: 2112

Alfa AF: 0.458 Hom.: 2133

Bravo AF: 0.366

Asia WGS AF: 0.404 AC: 1404 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	5.0
DANN	Benign	0.65
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs12725861; hg19: chr1-89566096; COSMIC: COSV71575918;