rs10493258

Positions:

• chr1-59200098-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000647858.1(FGGY-DT):​n.1955-66768C>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 0.0739 in 152,228 control chromosomes in the GnomAD database, including 620 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 0.074 (620 hom., cov: 32)
• Consequence: FGGY-DT ENST00000647858.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.225

Genes affected

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

LINC01358 (HGNC:50589): (long intergenic non-protein coding RNA 1358)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.149 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.1955-66768C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0737 AC: 11213 AN: 152110 Hom.: 619 Cov.: 32

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0567

Gnomad ASJ AF: 0.0459

Gnomad EAS AF: 0.000962

Gnomad SAS AF: 0.0261

Gnomad FIN AF: 0.0167

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0499

Gnomad OTH AF: 0.0880

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

GnomAD4 genome AF: 0.0739 AC: 11247 AN: 152228 Hom.: 620 Cov.: 32 AF XY: 0.0704 AC XY: 5243 AN XY: 74432

Gnomad4 AFR AF: 0.152

Gnomad4 AMR AF: 0.0568

Gnomad4 ASJ AF: 0.0459

Gnomad4 EAS AF: 0.000964

Gnomad4 SAS AF: 0.0259

Gnomad4 FIN AF: 0.0167

Gnomad4 NFE AF: 0.0499

Gnomad4 OTH AF: 0.0875

Alfa AF: 0.0574 Hom.: 621

Bravo AF: 0.0813

Asia WGS AF: 0.0210 AC: 75 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.90
DANN	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10493258; hg19: chr1-59665770;