rs1859524

Positions:

• chr7-47000577-G-A

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 0.32 in 152,048 control chromosomes in the GnomAD database, including 8,529 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 0.32 (8529 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.397

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.421 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.47000577G>A		intergenic_region
LOC105375268	XR_927249.1	n.*43C>T		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000223829	ENST00000423781.1	n.308-25560G>A		intron_variant		3
ENSG00000232072	ENST00000433337.1	n.237+48865C>T		intron_variant		3
ENSG00000229192	ENST00000412996.1	n.*44C>T		downstream_gene_variant		3
ENSG00000229192	ENST00000455078.5	n.*43C>T		downstream_gene_variant		3

Frequencies

GnomAD3 genomes AF: 0.320 AC: 48582 AN: 151930 Hom.: 8536 Cov.: 33

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.341

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.320 AC: 48584 AN: 152048 Hom.: 8529 Cov.: 33 AF XY: 0.314 AC XY: 23312 AN XY: 74304

Gnomad4 AFR AF: 0.186

Gnomad4 AMR AF: 0.376

Gnomad4 ASJ AF: 0.352

Gnomad4 EAS AF: 0.244

Gnomad4 SAS AF: 0.437

Gnomad4 FIN AF: 0.231

Gnomad4 NFE AF: 0.398

Gnomad4 OTH AF: 0.341

Alfa AF: 0.388 Hom.: 15606

Bravo AF: 0.320

Asia WGS AF: 0.337 AC: 1175 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.4
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1859524; hg19: chr7-47040175;