ENST00000647858.1:n.1954+53069A>G

Variant names:

• chr1-59237125-T-C
• rs6700125
• ENST00000647858.1:n.1954+53069A>G

Variant summary

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

The ENST00000647858.1(FGGY-DT):​n.1954+53069A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.578 in 151,916 control chromosomes in the GnomAD database, including 26,466 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 (26466 hom., cov: 31)
• Consequence: FGGY-DT ENST00000647858.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.642
• Publications: 6 publications found

Genes affected

FGGY-DT (HGNC:55265): (FGGY divergent transcript)

JUN-DT (HGNC:49450): (JUN divergent transcript)

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 (AMR) allele frequency at 95% confidence interval = 0.66 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000647858.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FGGY-DT	ENST00000647858.1		n.1954+53069A>G		intron	N/A
	JUN-DT	ENST00000715638.1		n.627-3183T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.578 AC: 87791 AN: 151798 Hom.: 26452 Cov.: 31

Gnomad AFR AF: 0.401

Gnomad AMI AF: 0.608

Gnomad AMR AF: 0.671

Gnomad ASJ AF: 0.554

Gnomad EAS AF: 0.498

Gnomad SAS AF: 0.580

Gnomad FIN AF: 0.694

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.654

Gnomad OTH AF: 0.588

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

GnomAD4 genome AF: 0.578 AC: 87824 AN: 151916 Hom.: 26466 Cov.: 31 AF XY: 0.580 AC XY: 43041 AN XY: 74238

African (AFR) AF: 0.400 AC: 16582 AN: 41410

American (AMR) AF: 0.671 AC: 10225 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.554 AC: 1922 AN: 3470

East Asian (EAS) AF: 0.498 AC: 2577 AN: 5170

South Asian (SAS) AF: 0.581 AC: 2802 AN: 4822

European-Finnish (FIN) AF: 0.694 AC: 7321 AN: 10542

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.654 AC: 44431 AN: 67958

Other (OTH) AF: 0.588 AC: 1241 AN: 2110

Alfa AF: 0.626 Hom.: 97227

Bravo AF: 0.572

Asia WGS AF: 0.581 AC: 2023 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	0.88
DANN	Benign	0.26
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs6700125; hg19: chr1-59702797;