rs7859473

Positions:

• chr9-132592859-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0261 in 152,224 control chromosomes in the GnomAD database, including 104 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 0.026 (104 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.996

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0261 (3975/152224) while in subpopulation AFR AF= 0.0248 (1029/41540). AF 95% confidence interval is 0.0235. There are 104 homozygotes in gnomad4. There are 2139 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 104 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.132592859T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0261 AC: 3969 AN: 152108 Hom.: 103 Cov.: 32

Gnomad AFR AF: 0.0248

Gnomad AMI AF: 0.0702

Gnomad AMR AF: 0.00720

Gnomad ASJ AF: 0.0101

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.00207

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0233

Gnomad OTH AF: 0.0177

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 4 Hom.: 0 AC XY: 0 AN XY: 0

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0261 AC: 3975 AN: 152224 Hom.: 104 Cov.: 32 AF XY: 0.0287 AC XY: 2139 AN XY: 74422

Gnomad4 AFR AF: 0.0248

Gnomad4 AMR AF: 0.00719

Gnomad4 ASJ AF: 0.0101

Gnomad4 EAS AF: 0.00154

Gnomad4 SAS AF: 0.00208

Gnomad4 FIN AF: 0.103

Gnomad4 NFE AF: 0.0233

Gnomad4 OTH AF: 0.0194

Alfa AF: 0.0324 Hom.: 26

Bravo AF: 0.0180

Asia WGS AF: 0.0170 AC: 58 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	2.6
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7859473; hg19: chr9-135468246;