10-128620973-A-G

Variant names:

• chr10-128620973-A-G
• rs10829448

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 0.0857 in 152,256 control chromosomes in the GnomAD database, including 766 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 0.086 (766 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.485

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.124 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: 0.0857 AC: 13044 AN: 152138 Hom.: 765 Cov.: 33

Gnomad AFR AF: 0.0272

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.0827

Gnomad ASJ AF: 0.100

Gnomad EAS AF: 0.00289

Gnomad SAS AF: 0.0713

Gnomad FIN AF: 0.0914

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.0793

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

GnomAD4 genome AF: 0.0857 AC: 13047 AN: 152256 Hom.: 766 Cov.: 33 AF XY: 0.0831 AC XY: 6187 AN XY: 74452

Gnomad4 AFR AF: 0.0271

Gnomad4 AMR AF: 0.0830

Gnomad4 ASJ AF: 0.100

Gnomad4 EAS AF: 0.00309

Gnomad4 SAS AF: 0.0707

Gnomad4 FIN AF: 0.0914

Gnomad4 NFE AF: 0.126

Gnomad4 OTH AF: 0.0790

Alfa AF: 0.0455 Hom.: 43

Bravo AF: 0.0837

Asia WGS AF: 0.0360 AC: 125 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.86
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10829448; hg19: chr10-130419237;