ENST00000647858.1:n.1954+11952C>T

Variant names:

• chr1-59278242-G-A
• rs333662
• ENST00000647858.1:n.1954+11952C>T

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+11952C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.808 in 152,208 control chromosomes in the GnomAD database, including 50,075 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 0.81 (50075 hom., cov: 33)
• Consequence: FGGY-DT ENST00000647858.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.160
• Publications: 1 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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FGGY-DT	ENST00000647858.1	n.1954+11952C>T		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.807 AC: 122807 AN: 152090 Hom.: 50029 Cov.: 33

Gnomad AFR AF: 0.687

Gnomad AMI AF: 0.875

Gnomad AMR AF: 0.852

Gnomad ASJ AF: 0.753

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.856

Gnomad FIN AF: 0.886

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.844

Gnomad OTH AF: 0.785

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

GnomAD4 genome AF: 0.808 AC: 122915 AN: 152208 Hom.: 50075 Cov.: 33 AF XY: 0.812 AC XY: 60429 AN XY: 74430

African (AFR) AF: 0.687 AC: 28515 AN: 41492

American (AMR) AF: 0.852 AC: 13041 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.753 AC: 2610 AN: 3468

East Asian (EAS) AF: 0.998 AC: 5173 AN: 5184

South Asian (SAS) AF: 0.856 AC: 4134 AN: 4830

European-Finnish (FIN) AF: 0.886 AC: 9395 AN: 10600

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.844 AC: 57391 AN: 68012

Other (OTH) AF: 0.787 AC: 1663 AN: 2112

Alfa AF: 0.824 Hom.: 75818

Bravo AF: 0.800

Asia WGS AF: 0.925 AC: 3215 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.85
DANN	Benign	0.51
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs333662; hg19: chr1-59743914;