rs2453556

Positions:

• chr9-27586164-A-G
• chr9-27586164-A-T

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 0.457 in 151,930 control chromosomes in the GnomAD database, including 16,362 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 0.46 (16362 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.816

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.578 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.27586164A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.456 AC: 69286 AN: 151812 Hom.: 16335 Cov.: 31

Gnomad AFR AF: 0.584

Gnomad AMI AF: 0.475

Gnomad AMR AF: 0.435

Gnomad ASJ AF: 0.319

Gnomad EAS AF: 0.463

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.403

Gnomad MID AF: 0.360

Gnomad NFE AF: 0.403

Gnomad OTH AF: 0.443

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

GnomAD4 genome AF: 0.457 AC: 69370 AN: 151930 Hom.: 16362 Cov.: 31 AF XY: 0.456 AC XY: 33872 AN XY: 74302

Gnomad4 AFR AF: 0.584

Gnomad4 AMR AF: 0.435

Gnomad4 ASJ AF: 0.319

Gnomad4 EAS AF: 0.463

Gnomad4 SAS AF: 0.407

Gnomad4 FIN AF: 0.403

Gnomad4 NFE AF: 0.403

Gnomad4 OTH AF: 0.443

Alfa AF: 0.412 Hom.: 28315

Bravo AF: 0.467

Asia WGS AF: 0.455 AC: 1585 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	14
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2453556; hg19: chr9-27586162;