rs7336303

Positions:

• chr13-45084799-C-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 0.146 in 152,150 control chromosomes in the GnomAD database, including 4,338 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 0.15 (4338 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.441 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.45084799C>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22163 AN: 152032 Hom.: 4341 Cov.: 32

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0963

Gnomad ASJ AF: 0.0109

Gnomad EAS AF: 0.0901

Gnomad SAS AF: 0.0425

Gnomad FIN AF: 0.00877

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0165

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.146 AC: 22200 AN: 152150 Hom.: 4338 Cov.: 32 AF XY: 0.144 AC XY: 10688 AN XY: 74366

Gnomad4 AFR AF: 0.447

Gnomad4 AMR AF: 0.0965

Gnomad4 ASJ AF: 0.0109

Gnomad4 EAS AF: 0.0903

Gnomad4 SAS AF: 0.0428

Gnomad4 FIN AF: 0.00877

Gnomad4 NFE AF: 0.0165

Gnomad4 OTH AF: 0.121

Alfa AF: 0.0390 Hom.: 836

Bravo AF: 0.166

Asia WGS AF: 0.0920 AC: 321 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.57
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7336303; hg19: chr13-45658934;