1-59223276-C-T

Variant names:

• chr1-59223276-C-T
• rs10493256
• ENST00000647858.1:n.1954+66918G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000647858.1(FGGY-DT):​n.1954+66918G>A variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.221
• Publications: 6 publications found

Genes affected

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

JUN-DT (HGNC:49450): (JUN divergent transcript)

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FGGY-DT	ENST00000647858.1	n.1954+66918G>A		intron_variant	Intron 3 of 4
JUN-DT	ENST00000715638.1	n.627-17032C>T		intron_variant	Intron 4 of 4

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

African (AFR) AF: 0.104 AC: 4306 AN: 41502

American (AMR) AF: 0.160 AC: 2445 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.169 AC: 586 AN: 3470

East Asian (EAS) AF: 0.170 AC: 877 AN: 5166

South Asian (SAS) AF: 0.165 AC: 796 AN: 4828

European-Finnish (FIN) AF: 0.290 AC: 3074 AN: 10588

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.286 AC: 19422 AN: 67960

Other (OTH) AF: 0.192 AC: 407 AN: 2116

Alfa AF: 0.242 Hom.: 6299

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
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs10493256; hg19: chr1-59688948;