chr19-51293045-T-C

Variant names:

• chr19-51293045-T-C
• rs10414689

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 0.108 in 152,224 control chromosomes in the GnomAD database, including 2,611 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 0.11 (2611 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.09).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.347 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: 0.108 AC: 16392 AN: 152106 Hom.: 2593 Cov.: 32

Gnomad AFR AF: 0.351

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.0470

Gnomad ASJ AF: 0.0213

Gnomad EAS AF: 0.00269

Gnomad SAS AF: 0.0375

Gnomad FIN AF: 0.000282

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0101

Gnomad OTH AF: 0.0765

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

GnomAD4 genome AF: 0.108 AC: 16466 AN: 152224 Hom.: 2611 Cov.: 32 AF XY: 0.105 AC XY: 7851 AN XY: 74452

Gnomad4 AFR AF: 0.352

Gnomad4 AMR AF: 0.0469

Gnomad4 ASJ AF: 0.0213

Gnomad4 EAS AF: 0.00270

Gnomad4 SAS AF: 0.0376

Gnomad4 FIN AF: 0.000282

Gnomad4 NFE AF: 0.0101

Gnomad4 OTH AF: 0.0823

Alfa AF: 0.0600 Hom.: 417

Bravo AF: 0.121

Asia WGS AF: 0.0820 AC: 287 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.44
DANN	Benign	0.15

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10414689; hg19: chr19-51796299;