13-97904022-C-A

Variant names:

• chr13-97904022-C-A
• rs1933121

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 0.218 in 152,110 control chromosomes in the GnomAD database, including 4,247 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 0.22 (4247 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.448

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.611 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: 0.218 AC: 33156 AN: 151992 Hom.: 4243 Cov.: 33

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.630

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.299

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.257

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

GnomAD4 genome AF: 0.218 AC: 33174 AN: 152110 Hom.: 4247 Cov.: 33 AF XY: 0.222 AC XY: 16500 AN XY: 74350

Gnomad4 AFR AF: 0.242

Gnomad4 AMR AF: 0.211

Gnomad4 ASJ AF: 0.235

Gnomad4 EAS AF: 0.629

Gnomad4 SAS AF: 0.305

Gnomad4 FIN AF: 0.183

Gnomad4 NFE AF: 0.170

Gnomad4 OTH AF: 0.261

Alfa AF: 0.184 Hom.: 353

Bravo AF: 0.224

Asia WGS AF: 0.457 AC: 1586 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.8
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1933121; hg19: chr13-98556276;