13-83957536-G-C

Variant names:

• chr13-83957536-G-C
• rs9319006

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;