1-22302564-A-G

Variant names:

• chr1-22302564-A-G
• rs6426746
• ENST00000788801.1:n.452+14037A>G

Variant summary

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

The ENST00000788801.1(ENSG00000302675):​n.452+14037A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.838 in 151,886 control chromosomes in the GnomAD database, including 53,422 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 0.84 (53422 hom., cov: 29)
• Consequence: ENSG00000302675 ENST00000788801.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.745
• Publications: 7 publications found

Genes affected

ENSG00000302675 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.918 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000788801.1. 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
	ENSG00000302675	ENST00000788801.1		n.452+14037A>G		intron	N/A
	ENSG00000302675	ENST00000788802.1		n.341+14037A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.838 AC: 127149 AN: 151768 Hom.: 53369 Cov.: 29

Gnomad AFR AF: 0.862

Gnomad AMI AF: 0.877

Gnomad AMR AF: 0.868

Gnomad ASJ AF: 0.713

Gnomad EAS AF: 0.940

Gnomad SAS AF: 0.852

Gnomad FIN AF: 0.817

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.817

Gnomad OTH AF: 0.844

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

GnomAD4 genome AF: 0.838 AC: 127259 AN: 151886 Hom.: 53422 Cov.: 29 AF XY: 0.840 AC XY: 62324 AN XY: 74208

African (AFR) AF: 0.862 AC: 35665 AN: 41382

American (AMR) AF: 0.868 AC: 13259 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.713 AC: 2476 AN: 3472

East Asian (EAS) AF: 0.940 AC: 4855 AN: 5166

South Asian (SAS) AF: 0.852 AC: 4086 AN: 4798

European-Finnish (FIN) AF: 0.817 AC: 8585 AN: 10512

Middle Eastern (MID) AF: 0.810 AC: 238 AN: 294

European-Non Finnish (NFE) AF: 0.817 AC: 55512 AN: 67964

Other (OTH) AF: 0.846 AC: 1785 AN: 2110

Alfa AF: 0.824 Hom.: 173193

Bravo AF: 0.846

Asia WGS AF: 0.888 AC: 3087 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.25
DANN	Benign	0.57
PhyloP100		-0.74

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: rs6426746;

hg19: chr1-22629057;