rs1998345

chr10-122364790-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 0.715 in 152,170 control chromosomes in the GnomAD database, including 39,748 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 0.71 (39748 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.702

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.866 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: 0.715 AC: 108685 AN: 152052 Hom.: 39698 Cov.: 33

Gnomad AFR AF: 0.873

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.688

Gnomad ASJ AF: 0.668

Gnomad EAS AF: 0.701

Gnomad SAS AF: 0.632

Gnomad FIN AF: 0.632

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.649

Gnomad OTH AF: 0.698

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

GnomAD4 genome AF: 0.715 AC: 108790 AN: 152170 Hom.: 39748 Cov.: 33 AF XY: 0.713 AC XY: 53066 AN XY: 74386

Gnomad4 AFR AF: 0.873

Gnomad4 AMR AF: 0.687

Gnomad4 ASJ AF: 0.668

Gnomad4 EAS AF: 0.701

Gnomad4 SAS AF: 0.632

Gnomad4 FIN AF: 0.632

Gnomad4 NFE AF: 0.649

Gnomad4 OTH AF: 0.702

Alfa AF: 0.660 Hom.: 42587

Bravo AF: 0.730

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.14
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: rs1998345; hg19: chr10-124124306;