rs10439163

chr19-10534819-A-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 0.457 in 151,850 control chromosomes in the GnomAD database, including 16,642 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 0.46 (16642 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.88

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.83 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: 0.456 AC: 69261 AN: 151730 Hom.: 16627 Cov.: 31

Gnomad AFR AF: 0.414

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.581

Gnomad ASJ AF: 0.482

Gnomad EAS AF: 0.851

Gnomad SAS AF: 0.590

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.473

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

GnomAD4 genome AF: 0.457 AC: 69322 AN: 151850 Hom.: 16642 Cov.: 31 AF XY: 0.464 AC XY: 34396 AN XY: 74164

Gnomad4 AFR AF: 0.415

Gnomad4 AMR AF: 0.581

Gnomad4 ASJ AF: 0.482

Gnomad4 EAS AF: 0.851

Gnomad4 SAS AF: 0.589

Gnomad4 FIN AF: 0.386

Gnomad4 NFE AF: 0.423

Gnomad4 OTH AF: 0.471

Alfa AF: 0.439 Hom.: 2668

Bravo AF: 0.470

Asia WGS AF: 0.660 AC: 2292 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	1.1
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10439163; hg19: chr19-10645495;