rs4354815

Positions:

• chr13-80993818-A-G

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 0.0547 in 152,256 control chromosomes in the GnomAD database, including 458 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 0.055 (458 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.164

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.137 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.80993818A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000286746	ENST00000655229.1	n.43-7339T>C		intron_variant
ENSG00000286746	ENST00000660876.1	n.53+23862T>C		intron_variant
ENSG00000286746	ENST00000661648.1	n.30+23862T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0547 AC: 8317 AN: 152138 Hom.: 461 Cov.: 32

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.0317

Gnomad ASJ AF: 0.0741

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0168

Gnomad FIN AF: 0.00283

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0217

Gnomad OTH AF: 0.0487

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

GnomAD4 genome AF: 0.0547 AC: 8321 AN: 152256 Hom.: 458 Cov.: 32 AF XY: 0.0525 AC XY: 3910 AN XY: 74446

Gnomad4 AFR AF: 0.140

Gnomad4 AMR AF: 0.0317

Gnomad4 ASJ AF: 0.0741

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0170

Gnomad4 FIN AF: 0.00283

Gnomad4 NFE AF: 0.0217

Gnomad4 OTH AF: 0.0482

Alfa AF: 0.0379 Hom.: 29

Bravo AF: 0.0621

Asia WGS AF: 0.0190 AC: 64 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.75
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4354815; hg19: chr13-81567953;