1-59239775-A-C

Position:

• chr1-59239775-A-C

Variant summary

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

The ENST00000647858.1(FGGY-DT):​n.1954+50419T>G 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 0.736 in 152,030 control chromosomes in the GnomAD database, including 41,398 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 0.74 (41398 hom., cov: 32)
• Consequence: FGGY-DT ENST00000647858.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.779

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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.849 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FGGY-DT	ENST00000647858.1	n.1954+50419T>G		intron_variant, non_coding_transcript_variant
LINC01358	ENST00000625548.1	n.627-533A>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.736 AC: 111840 AN: 151912 Hom.: 41358 Cov.: 32

Gnomad AFR AF: 0.678

Gnomad AMI AF: 0.718

Gnomad AMR AF: 0.801

Gnomad ASJ AF: 0.644

Gnomad EAS AF: 0.870

Gnomad SAS AF: 0.795

Gnomad FIN AF: 0.801

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.739

Gnomad OTH AF: 0.724

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

GnomAD4 genome AF: 0.736 AC: 111933 AN: 152030 Hom.: 41398 Cov.: 32 AF XY: 0.741 AC XY: 55051 AN XY: 74310

Gnomad4 AFR AF: 0.678

Gnomad4 AMR AF: 0.802

Gnomad4 ASJ AF: 0.644

Gnomad4 EAS AF: 0.870

Gnomad4 SAS AF: 0.795

Gnomad4 FIN AF: 0.801

Gnomad4 NFE AF: 0.739

Gnomad4 OTH AF: 0.725

Alfa AF: 0.736 Hom.: 39638

Bravo AF: 0.734

Asia WGS AF: 0.851 AC: 2959 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.2
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6587852; hg19: chr1-59705447;