rs9576235

Positions:

• chr13-37276569-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 0.282 in 152,084 control chromosomes in the GnomAD database, including 7,339 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 0.28 (7339 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.152

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.38 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.37276569G>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.282 AC: 42900 AN: 151964 Hom.: 7344 Cov.: 32

Gnomad AFR AF: 0.0822

Gnomad AMI AF: 0.530

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.394

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.357

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.367

Gnomad OTH AF: 0.281

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

GnomAD4 genome AF: 0.282 AC: 42892 AN: 152084 Hom.: 7339 Cov.: 32 AF XY: 0.285 AC XY: 21152 AN XY: 74338

Gnomad4 AFR AF: 0.0820

Gnomad4 AMR AF: 0.344

Gnomad4 ASJ AF: 0.296

Gnomad4 EAS AF: 0.395

Gnomad4 SAS AF: 0.266

Gnomad4 FIN AF: 0.357

Gnomad4 NFE AF: 0.367

Gnomad4 OTH AF: 0.279

Alfa AF: 0.335 Hom.: 4518

Bravo AF: 0.271

Asia WGS AF: 0.309 AC: 1076 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.3
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9576235; hg19: chr13-37850706;