chr10-128620973-A-G

Variant names:

• chr10-128620973-A-G
• rs10829448

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0271 AC: 1127 AN: 41558

American (AMR) AF: 0.0830 AC: 1270 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.100 AC: 348 AN: 3472

East Asian (EAS) AF: 0.00309 AC: 16 AN: 5180

South Asian (SAS) AF: 0.0707 AC: 341 AN: 4824

European-Finnish (FIN) AF: 0.0914 AC: 970 AN: 10614

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.126 AC: 8567 AN: 67988

Other (OTH) AF: 0.0790 AC: 167 AN: 2114

Alfa AF: 0.0687 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
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs10829448; hg19: chr10-130419237;