rs2320597

Variant names:

• chr13-21959469-C-A
• rs2320597

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 0.0486 in 152,122 control chromosomes in the GnomAD database, including 512 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 0.049 (512 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.867

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.326 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: 0.0484 AC: 7356 AN: 152006 Hom.: 507 Cov.: 32

Gnomad AFR AF: 0.0762

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0750

Gnomad ASJ AF: 0.0170

Gnomad EAS AF: 0.338

Gnomad SAS AF: 0.0796

Gnomad FIN AF: 0.0103

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.00981

Gnomad OTH AF: 0.0387

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

GnomAD4 genome AF: 0.0486 AC: 7390 AN: 152122 Hom.: 512 Cov.: 32 AF XY: 0.0525 AC XY: 3901 AN XY: 74374

Gnomad4 AFR AF: 0.0767

Gnomad4 AMR AF: 0.0750

Gnomad4 ASJ AF: 0.0170

Gnomad4 EAS AF: 0.339

Gnomad4 SAS AF: 0.0799

Gnomad4 FIN AF: 0.0103

Gnomad4 NFE AF: 0.00981

Gnomad4 OTH AF: 0.0402

Alfa AF: 0.0208 Hom.: 310

Bravo AF: 0.0557

Asia WGS AF: 0.182 AC: 633 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.042
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2320597; hg19: chr13-22533608;