chr1-59199870-A-G

Position:

• chr1-59199870-A-G

Variant summary

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

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.898

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.59199870A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FGGY-DT	ENST00000623433.3	n.307+3225T>C		intron_variant		5
FGGY-DT	ENST00000624265.3	n.111+8141T>C		intron_variant		5
FGGY-DT	ENST00000624582.3	n.374+3225T>C		intron_variant		5

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

Gnomad4 AFR AF: 0.423

Gnomad4 AMR AF: 0.685

Gnomad4 ASJ AF: 0.662

Gnomad4 EAS AF: 0.531

Gnomad4 SAS AF: 0.658

Gnomad4 FIN AF: 0.641

Gnomad4 NFE AF: 0.604

Gnomad4 OTH AF: 0.608

Alfa AF: 0.607 Hom.: 58488

Bravo AF: 0.566

Asia WGS AF: 0.598 AC: 2078 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs331635; hg19: chr1-59665542;