chr10-130884466-T-C

Position:

• chr10-130884466-T-C

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 0.756 in 152,116 control chromosomes in the GnomAD database, including 43,796 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 0.76 (43796 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.63

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.86 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: 0.756 AC: 114980 AN: 151998 Hom.: 43789 Cov.: 32

Gnomad AFR AF: 0.660

Gnomad AMI AF: 0.738

Gnomad AMR AF: 0.835

Gnomad ASJ AF: 0.806

Gnomad EAS AF: 0.882

Gnomad SAS AF: 0.730

Gnomad FIN AF: 0.813

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.779

Gnomad OTH AF: 0.765

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

GnomAD4 genome AF: 0.756 AC: 115036 AN: 152116 Hom.: 43796 Cov.: 32 AF XY: 0.758 AC XY: 56364 AN XY: 74366

Gnomad4 AFR AF: 0.660

Gnomad4 AMR AF: 0.836

Gnomad4 ASJ AF: 0.806

Gnomad4 EAS AF: 0.881

Gnomad4 SAS AF: 0.728

Gnomad4 FIN AF: 0.813

Gnomad4 NFE AF: 0.778

Gnomad4 OTH AF: 0.762

Alfa AF: 0.777 Hom.: 93204

Bravo AF: 0.754

Asia WGS AF: 0.798 AC: 2778 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.035
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: rs4751295; hg19: chr10-132682729;