rs6587852

Variant names:

• chr1-59239775-A-C
• rs6587852
• ENST00000647858.1:n.1954+50419T>G

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000647858.1(FGGY-DT):​n.1954+50419T>G 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: FGGY-DT ENST00000647858.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.779
• Publications: 1 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 -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000647858.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FGGY-DT	ENST00000647858.1		n.1954+50419T>G		intron	N/A
	JUN-DT	ENST00000715638.1		n.627-533A>C		intron	N/A

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

African (AFR) AF: 0.678 AC: 28093 AN: 41448

American (AMR) AF: 0.802 AC: 12240 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.644 AC: 2233 AN: 3466

East Asian (EAS) AF: 0.870 AC: 4502 AN: 5176

South Asian (SAS) AF: 0.795 AC: 3830 AN: 4820

European-Finnish (FIN) AF: 0.801 AC: 8473 AN: 10584

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.739 AC: 50186 AN: 67952

Other (OTH) AF: 0.725 AC: 1532 AN: 2112

Alfa AF: 0.735 Hom.: 52188

Bravo AF: 0.734

Asia WGS AF: 0.851 AC: 2959 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.2
DANN	Benign	0.66
PhyloP100		-0.78

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6587852;

hg19: chr1-59705447;