rs10414689

Positions:

• chr19-51293045-T-C
• chr19-51293045-T-G

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;