13-82475190-G-C

Variant names:

• chr13-82475190-G-C
• rs9318868

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 0.329 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.329 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

Gnomad4 AFR AF: 0.270

Gnomad4 AMR AF: 0.391

Gnomad4 ASJ AF: 0.446

Gnomad4 EAS AF: 0.512

Gnomad4 SAS AF: 0.303

Gnomad4 FIN AF: 0.253

Gnomad4 NFE AF: 0.342

Gnomad4 OTH AF: 0.381

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9318868; hg19: chr13-83049325;