rs13394720

Positions:

• chr2-233593475-T-C

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 0.068 in 152,166 control chromosomes in the GnomAD database, including 556 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 0.068 (556 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.85

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.149 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0678 AC: 10310 AN: 152048 Hom.: 550 Cov.: 32

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.0746

Gnomad AMR AF: 0.0376

Gnomad ASJ AF: 0.0357

Gnomad EAS AF: 0.0655

Gnomad SAS AF: 0.0338

Gnomad FIN AF: 0.0405

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0323

Gnomad OTH AF: 0.0611

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

GnomAD4 genome AF: 0.0680 AC: 10348 AN: 152166 Hom.: 556 Cov.: 32 AF XY: 0.0675 AC XY: 5019 AN XY: 74410

Gnomad4 AFR AF: 0.152

Gnomad4 AMR AF: 0.0376

Gnomad4 ASJ AF: 0.0357

Gnomad4 EAS AF: 0.0653

Gnomad4 SAS AF: 0.0339

Gnomad4 FIN AF: 0.0405

Gnomad4 NFE AF: 0.0323

Gnomad4 OTH AF: 0.0600

Alfa AF: 0.0393 Hom.: 175

Bravo AF: 0.0718

Asia WGS AF: 0.0550 AC: 193 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.28
DANN	Benign	0.14

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13394720; hg19: chr2-234502121;