13-83957536-G-C

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 0.0884 in 151,610 control chromosomes in the GnomAD database, including 730 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 0.088 (730 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.171

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.126 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0884 AC: 13398 AN: 151496 Hom.: 730 Cov.: 32

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.0822

Gnomad AMR AF: 0.0908

Gnomad ASJ AF: 0.0781

Gnomad EAS AF: 0.00117

Gnomad SAS AF: 0.0315

Gnomad FIN AF: 0.0296

Gnomad MID AF: 0.103

Gnomad NFE AF: 0.0838

Gnomad OTH AF: 0.0876

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

GnomAD4 genome AF: 0.0884 AC: 13407 AN: 151610 Hom.: 730 Cov.: 32 AF XY: 0.0855 AC XY: 6329 AN XY: 74050

Gnomad4 AFR AF: 0.128

Gnomad4 AMR AF: 0.0907

Gnomad4 ASJ AF: 0.0781

Gnomad4 EAS AF: 0.00117

Gnomad4 SAS AF: 0.0315

Gnomad4 FIN AF: 0.0296

Gnomad4 NFE AF: 0.0839

Gnomad4 OTH AF: 0.0867

Alfa AF: 0.0776 Hom.: 59

Bravo AF: 0.0970

Asia WGS AF: 0.0200 AC: 71 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.34
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9319006; hg19: chr13-84531671;