10-106366383-C-T

Position:

• chr10-106366383-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 0.863 in 152,172 control chromosomes in the GnomAD database, including 56,890 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 0.86 (56890 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.932 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: 0.863 AC: 131210 AN: 152052 Hom.: 56821 Cov.: 31

Gnomad AFR AF: 0.940

Gnomad AMI AF: 0.810

Gnomad AMR AF: 0.860

Gnomad ASJ AF: 0.784

Gnomad EAS AF: 0.709

Gnomad SAS AF: 0.831

Gnomad FIN AF: 0.839

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.840

Gnomad OTH AF: 0.848

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

GnomAD4 genome AF: 0.863 AC: 131336 AN: 152172 Hom.: 56890 Cov.: 31 AF XY: 0.861 AC XY: 64025 AN XY: 74396

Gnomad4 AFR AF: 0.940

Gnomad4 AMR AF: 0.860

Gnomad4 ASJ AF: 0.784

Gnomad4 EAS AF: 0.708

Gnomad4 SAS AF: 0.832

Gnomad4 FIN AF: 0.839

Gnomad4 NFE AF: 0.840

Gnomad4 OTH AF: 0.845

Alfa AF: 0.853 Hom.: 10441

Bravo AF: 0.868

Asia WGS AF: 0.783 AC: 2727 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.041
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs821677; hg19: chr10-108126141;