13-83957536-G-C

Variant names:

• chr13-83957536-G-C
• rs9319006

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.128 AC: 5309 AN: 41328

American (AMR) AF: 0.0907 AC: 1382 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.0781 AC: 271 AN: 3470

East Asian (EAS) AF: 0.00117 AC: 6 AN: 5132

South Asian (SAS) AF: 0.0315 AC: 151 AN: 4796

European-Finnish (FIN) AF: 0.0296 AC: 310 AN: 10458

Middle Eastern (MID) AF: 0.0966 AC: 28 AN: 290

European-Non Finnish (NFE) AF: 0.0839 AC: 5693 AN: 67892

Other (OTH) AF: 0.0867 AC: 182 AN: 2100

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.34
DANN	Benign	0.69
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs9319006; hg19: chr13-84531671;