13-82475190-G-C

Variant names:

• chr13-82475190-G-C
• rs9318868

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 0.329 in 150,912 control chromosomes in the GnomAD database, including 8,473 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 0.33 (8473 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0410
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.496 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.329 AC: 49623 AN: 150794 Hom.: 8474 Cov.: 32

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.381

Gnomad AMR AF: 0.391

Gnomad ASJ AF: 0.446

Gnomad EAS AF: 0.512

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.253

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.342

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.329 AC: 49635 AN: 150912 Hom.: 8473 Cov.: 32 AF XY: 0.327 AC XY: 24117 AN XY: 73654

African (AFR) AF: 0.270 AC: 11156 AN: 41306

American (AMR) AF: 0.391 AC: 5896 AN: 15072

Ashkenazi Jewish (ASJ) AF: 0.446 AC: 1539 AN: 3452

East Asian (EAS) AF: 0.512 AC: 2610 AN: 5096

South Asian (SAS) AF: 0.303 AC: 1458 AN: 4808

European-Finnish (FIN) AF: 0.253 AC: 2660 AN: 10530

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.342 AC: 23064 AN: 67356

Other (OTH) AF: 0.381 AC: 797 AN: 2090

Alfa AF: 0.199 Hom.: 405

Bravo AF: 0.343

Asia WGS AF: 0.422 AC: 1465 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	7.2
DANN	Benign	0.63
PhyloP100		0.041

Splicing

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

Other links and lift over

dbSNP: rs9318868; hg19: chr13-83049325;