rs10439163

Variant names:

• chr19-10534819-A-G
• rs10439163

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;