rs10999530

Positions:

• chr10-70767697-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0278 in 135,778 control chromosomes in the GnomAD database, including 41 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 0.028 (41 hom., cov: 26)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.507

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0278 (3780/135778) while in subpopulation NFE AF= 0.0416 (2450/58942). AF 95% confidence interval is 0.0402. There are 41 homozygotes in gnomad4. There are 1771 alleles in male gnomad4 subpopulation. Median coverage is 26. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 41 gene

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: 0.0279 AC: 3785 AN: 135640 Hom.: 40 Cov.: 26

Gnomad AFR AF: 0.00639

Gnomad AMI AF: 0.0798

Gnomad AMR AF: 0.0195

Gnomad ASJ AF: 0.0355

Gnomad EAS AF: 0.0321

Gnomad SAS AF: 0.0262

Gnomad FIN AF: 0.0390

Gnomad MID AF: 0.0278

Gnomad NFE AF: 0.0416

Gnomad OTH AF: 0.0276

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

GnomAD4 genome AF: 0.0278 AC: 3780 AN: 135778 Hom.: 41 Cov.: 26 AF XY: 0.0268 AC XY: 1771 AN XY: 66078

Gnomad4 AFR AF: 0.00637

Gnomad4 AMR AF: 0.0195

Gnomad4 ASJ AF: 0.0355

Gnomad4 EAS AF: 0.0319

Gnomad4 SAS AF: 0.0262

Gnomad4 FIN AF: 0.0390

Gnomad4 NFE AF: 0.0416

Gnomad4 OTH AF: 0.0273

Alfa AF: 0.0815 Hom.: 74

Bravo AF: 0.0696

Asia WGS AF: 0.0340 AC: 114 AN: 3340

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.3
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10999530; hg19: chr10-72527453;