rs333662

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr1-59278242-G-A
• chr1-59278242-G-C
• chr1-59278242-G-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.687

Gnomad4 AMR AF: 0.852

Gnomad4 ASJ AF: 0.753

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.856

Gnomad4 FIN AF: 0.886

Gnomad4 NFE AF: 0.844

Gnomad4 OTH AF: 0.787

Alfa AF: 0.826 Hom.: 51886

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs333662; hg19: chr1-59743914;