rs10493256

Positions:

• chr1-59223276-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000647858.1(FGGY-DT):​n.1954+66918G>A 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 0.211 in 152,126 control chromosomes in the GnomAD database, including 3,929 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 0.21 (3929 hom., cov: 32)
• Consequence: FGGY-DT ENST00000647858.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.221

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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.27).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.282 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+66918G>A		intron_variant, non_coding_transcript_variant
LINC01358	ENST00000625548.1	n.627-17032C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.211 AC: 32107 AN: 152008 Hom.: 3932 Cov.: 32

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.290

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.286

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.211 AC: 32134 AN: 152126 Hom.: 3929 Cov.: 32 AF XY: 0.208 AC XY: 15505 AN XY: 74378

Gnomad4 AFR AF: 0.104

Gnomad4 AMR AF: 0.160

Gnomad4 ASJ AF: 0.169

Gnomad4 EAS AF: 0.170

Gnomad4 SAS AF: 0.165

Gnomad4 FIN AF: 0.290

Gnomad4 NFE AF: 0.286

Gnomad4 OTH AF: 0.192

Alfa AF: 0.249 Hom.: 5037

Bravo AF: 0.199

Asia WGS AF: 0.167 AC: 580 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.27
CADD	Benign	17
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10493256; hg19: chr1-59688948;