1-59238310-G-A

Position:

• chr1-59238310-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.1954+51884C>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 0.629 in 151,898 control chromosomes in the GnomAD database, including 30,414 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 0.63 (30414 hom., cov: 31)
• Consequence: FGGY-DT ENST00000647858.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.882

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=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.705 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+51884C>T		intron_variant, non_coding_transcript_variant
LINC01358	ENST00000625548.1	n.627-1998G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.629 AC: 95507 AN: 151780 Hom.: 30393 Cov.: 31

Gnomad AFR AF: 0.527

Gnomad AMI AF: 0.615

Gnomad AMR AF: 0.716

Gnomad ASJ AF: 0.563

Gnomad EAS AF: 0.686

Gnomad SAS AF: 0.683

Gnomad FIN AF: 0.707

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.655

Gnomad OTH AF: 0.630

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

GnomAD4 genome AF: 0.629 AC: 95568 AN: 151898 Hom.: 30414 Cov.: 31 AF XY: 0.633 AC XY: 46959 AN XY: 74226

Gnomad4 AFR AF: 0.527

Gnomad4 AMR AF: 0.716

Gnomad4 ASJ AF: 0.563

Gnomad4 EAS AF: 0.686

Gnomad4 SAS AF: 0.683

Gnomad4 FIN AF: 0.707

Gnomad4 NFE AF: 0.655

Gnomad4 OTH AF: 0.632

Alfa AF: 0.646 Hom.: 33533

Bravo AF: 0.625

Asia WGS AF: 0.730 AC: 2538 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.6
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6690993; hg19: chr1-59703982;