rs333662

Positions:

• 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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FGGY-DT	ENST00000647858.1	n.1954+11952C>T		intron_variant, non_coding_transcript_variant

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;