1-59199870-A-G

Variant names:

• chr1-59199870-A-G
• rs331635
• ENST00000623433.4:n.307+3225T>C

Variant summary

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

The ENST00000647858.1(FGGY-DT):​n.1955-66540T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.567 in 152,042 control chromosomes in the GnomAD database, including 25,188 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 0.57 (25188 hom., cov: 32)
• Consequence: FGGY-DT ENST00000647858.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.898
• Publications: 5 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=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.674 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	ENST00000623433.4	TSL:5	n.307+3225T>C		intron	N/A
	FGGY-DT	ENST00000624265.3	TSL:5	n.111+8141T>C		intron	N/A
	FGGY-DT	ENST00000624582.3	TSL:5	n.374+3225T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.567 AC: 86150 AN: 151924 Hom.: 25178 Cov.: 32

Gnomad AFR AF: 0.424

Gnomad AMI AF: 0.730

Gnomad AMR AF: 0.685

Gnomad ASJ AF: 0.662

Gnomad EAS AF: 0.529

Gnomad SAS AF: 0.658

Gnomad FIN AF: 0.641

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.604

Gnomad OTH AF: 0.609

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

GnomAD4 genome AF: 0.567 AC: 86181 AN: 152042 Hom.: 25188 Cov.: 32 AF XY: 0.572 AC XY: 42537 AN XY: 74304

African (AFR) AF: 0.423 AC: 17561 AN: 41482

American (AMR) AF: 0.685 AC: 10468 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.662 AC: 2297 AN: 3470

East Asian (EAS) AF: 0.531 AC: 2741 AN: 5166

South Asian (SAS) AF: 0.658 AC: 3170 AN: 4820

European-Finnish (FIN) AF: 0.641 AC: 6762 AN: 10546

Middle Eastern (MID) AF: 0.690 AC: 203 AN: 294

European-Non Finnish (NFE) AF: 0.604 AC: 41028 AN: 67958

Other (OTH) AF: 0.608 AC: 1285 AN: 2112

Alfa AF: 0.595 Hom.: 122308

Bravo AF: 0.566

Asia WGS AF: 0.598 AC: 2078 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.5
DANN	Benign	0.73
PhyloP100		0.90

Splicing

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

Other links and lift over

dbSNP: rs331635; hg19: chr1-59665542;