chr10-128620973-A-G

Position:

• chr10-128620973-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 0.0857 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;