10-129466317-T-G

Position:

• chr10-129466317-T-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 0.702 in 151,938 control chromosomes in the GnomAD database, including 40,750 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 0.70 (40750 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.792

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.958 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.702 AC: 106642 AN: 151820 Hom.: 40742 Cov.: 31

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.853

Gnomad AMR AF: 0.798

Gnomad ASJ AF: 0.821

Gnomad EAS AF: 0.980

Gnomad SAS AF: 0.867

Gnomad FIN AF: 0.763

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.829

Gnomad OTH AF: 0.736

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

GnomAD4 genome AF: 0.702 AC: 106671 AN: 151938 Hom.: 40750 Cov.: 31 AF XY: 0.705 AC XY: 52357 AN XY: 74220

Gnomad4 AFR AF: 0.374

Gnomad4 AMR AF: 0.798

Gnomad4 ASJ AF: 0.821

Gnomad4 EAS AF: 0.981

Gnomad4 SAS AF: 0.867

Gnomad4 FIN AF: 0.763

Gnomad4 NFE AF: 0.829

Gnomad4 OTH AF: 0.737

Alfa AF: 0.759 Hom.: 12023

Bravo AF: 0.690

Asia WGS AF: 0.876 AC: 3046 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.5
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1711646; hg19: chr10-131264581;