rs6587852

Variant names:

• chr1-59239775-A-C
• rs6587852
• ENST00000625548.1:n.627-533A>C

Your query was ambiguous. Multiple possible variants found:

• chr1-59239775-A-C
• chr1-59239775-A-G

Variant summary

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

The ENST00000625548.1(LINC01358):​n.627-533A>C variant causes a intron 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: LINC01358 ENST00000625548.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.779

Genes affected

LINC01358 (HGNC:):

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

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01358	ENST00000625548.1	n.627-533A>C		intron_variant	Intron 4 of 4	5
FGGY-DT	ENST00000647858.1	n.1954+50419T>G		intron_variant	Intron 3 of 4

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;