10-130839042-C-T

Position:

• chr10-130839042-C-T

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 0.326 in 147,836 control chromosomes in the GnomAD database, including 10,693 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 0.33 (10693 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.209

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.385 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: 0.326 AC: 48222 AN: 147720 Hom.: 10694 Cov.: 28

Gnomad AFR AF: 0.184

Gnomad AMI AF: 0.206

Gnomad AMR AF: 0.381

Gnomad ASJ AF: 0.367

Gnomad EAS AF: 0.389

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.404

Gnomad MID AF: 0.349

Gnomad NFE AF: 0.389

Gnomad OTH AF: 0.369

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

GnomAD4 genome AF: 0.326 AC: 48235 AN: 147836 Hom.: 10693 Cov.: 28 AF XY: 0.325 AC XY: 23405 AN XY: 71976

Gnomad4 AFR AF: 0.184

Gnomad4 AMR AF: 0.381

Gnomad4 ASJ AF: 0.367

Gnomad4 EAS AF: 0.390

Gnomad4 SAS AF: 0.249

Gnomad4 FIN AF: 0.404

Gnomad4 NFE AF: 0.389

Gnomad4 OTH AF: 0.368

Alfa AF: 0.349 Hom.: 1332

Asia WGS AF: 0.313 AC: 1085 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.99
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7094308; hg19: chr10-132637305;