1-59249320-T-C

Variant names:

• chr1-59249320-T-C
• rs1470407
• ENST00000647858.1:n.1954+40874A>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+40874A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.781 in 152,088 control chromosomes in the GnomAD database, including 46,977 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 0.78 (46977 hom., cov: 32)
• Consequence: FGGY-DT ENST00000647858.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.572
• Publications: 2 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.835 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

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
	FGGY-DT	ENST00000647858.1		n.1954+40874A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.781 AC: 118663 AN: 151970 Hom.: 46949 Cov.: 32

Gnomad AFR AF: 0.637

Gnomad AMI AF: 0.866

Gnomad AMR AF: 0.846

Gnomad ASJ AF: 0.752

Gnomad EAS AF: 0.816

Gnomad SAS AF: 0.843

Gnomad FIN AF: 0.819

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.841

Gnomad OTH AF: 0.792

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

GnomAD4 genome AF: 0.781 AC: 118736 AN: 152088 Hom.: 46977 Cov.: 32 AF XY: 0.781 AC XY: 58079 AN XY: 74342

African (AFR) AF: 0.637 AC: 26412 AN: 41478

American (AMR) AF: 0.846 AC: 12916 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.752 AC: 2610 AN: 3470

East Asian (EAS) AF: 0.816 AC: 4220 AN: 5174

South Asian (SAS) AF: 0.843 AC: 4056 AN: 4814

European-Finnish (FIN) AF: 0.819 AC: 8664 AN: 10578

Middle Eastern (MID) AF: 0.755 AC: 222 AN: 294

European-Non Finnish (NFE) AF: 0.841 AC: 57168 AN: 67988

Other (OTH) AF: 0.794 AC: 1678 AN: 2114

Alfa AF: 0.824 Hom.: 196333

Bravo AF: 0.777

Asia WGS AF: 0.847 AC: 2945 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	7.7
DANN	Benign	0.52
PhyloP100		0.57

Splicing

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

Other links and lift over

dbSNP: rs1470407; hg19: chr1-59714992;