rs13411119

Positions:

• chr2-58251044-G-A
• chr2-58251044-G-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 0.411 in 151,948 control chromosomes in the GnomAD database, including 16,401 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 0.41 (16401 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.407

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.751 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.410 AC: 62309 AN: 151830 Hom.: 16362 Cov.: 32

Gnomad AFR AF: 0.758

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.242

Gnomad EAS AF: 0.280

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.351

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

GnomAD4 genome AF: 0.411 AC: 62416 AN: 151948 Hom.: 16401 Cov.: 32 AF XY: 0.408 AC XY: 30326 AN XY: 74276

Gnomad4 AFR AF: 0.758

Gnomad4 AMR AF: 0.283

Gnomad4 ASJ AF: 0.242

Gnomad4 EAS AF: 0.280

Gnomad4 SAS AF: 0.302

Gnomad4 FIN AF: 0.311

Gnomad4 NFE AF: 0.275

Gnomad4 OTH AF: 0.352

Alfa AF: 0.286 Hom.: 14057

Bravo AF: 0.422

Asia WGS AF: 0.359 AC: 1250 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.2
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13411119; hg19: chr2-58478179;