10-2107066-A-G

Position:

• chr10-2107066-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 0.77 in 152,138 control chromosomes in the GnomAD database, including 46,496 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 0.77 (46496 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.891 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: 0.770 AC: 117079 AN: 152020 Hom.: 46484 Cov.: 33

Gnomad AFR AF: 0.556

Gnomad AMI AF: 0.831

Gnomad AMR AF: 0.778

Gnomad ASJ AF: 0.824

Gnomad EAS AF: 0.913

Gnomad SAS AF: 0.855

Gnomad FIN AF: 0.838

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.867

Gnomad OTH AF: 0.782

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

GnomAD4 genome AF: 0.770 AC: 117147 AN: 152138 Hom.: 46496 Cov.: 33 AF XY: 0.770 AC XY: 57306 AN XY: 74376

Gnomad4 AFR AF: 0.556

Gnomad4 AMR AF: 0.778

Gnomad4 ASJ AF: 0.824

Gnomad4 EAS AF: 0.913

Gnomad4 SAS AF: 0.856

Gnomad4 FIN AF: 0.838

Gnomad4 NFE AF: 0.867

Gnomad4 OTH AF: 0.784

Alfa AF: 0.798 Hom.: 6127

Bravo AF: 0.760

Asia WGS AF: 0.845 AC: 2939 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.28
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs959702; hg19: chr10-2149260;