19-50902897-C-A

Variant names:

• chr19-50902897-C-A
• rs11881373

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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 0.35 (8000 hom., cov: 19)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.124

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.399 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: 0.347 AC: 44791 AN: 129024 Hom.: 7991 Cov.: 19

Gnomad AFR AF: 0.350

Gnomad AMI AF: 0.348

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.159

Gnomad SAS AF: 0.415

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.476

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.347 AC: 44824 AN: 129106 Hom.: 8000 Cov.: 19 AF XY: 0.344 AC XY: 20974 AN XY: 60918

Gnomad4 AFR AF: 0.350

Gnomad4 AMR AF: 0.332

Gnomad4 ASJ AF: 0.332

Gnomad4 EAS AF: 0.160

Gnomad4 SAS AF: 0.416

Gnomad4 FIN AF: 0.303

Gnomad4 NFE AF: 0.363

Gnomad4 OTH AF: 0.366

Alfa AF: 0.198 Hom.: 418

Bravo AF: 0.351

Asia WGS AF: 0.288 AC: 975 AN: 3380

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.2
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11881373; hg19: chr19-51406153;