rs6690993

Variant names:

• chr1-59238310-G-A
• rs6690993
• ENST00000625548.1:n.627-1998G>A

Your query was ambiguous. Multiple possible variants found:

• chr1-59238310-G-A
• chr1-59238310-G-C

Variant summary

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

The ENST00000625548.1(LINC01358):​n.627-1998G>A variant causes a intron 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: LINC01358 ENST00000625548.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.882

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=-0.81).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01358	ENST00000625548.1	n.627-1998G>A		intron_variant	Intron 4 of 4	5
FGGY-DT	ENST00000647858.1	n.1954+51884C>T		intron_variant	Intron 3 of 4

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;