rs1998345

Variant names:

• chr10-122364790-A-G
• rs1998345

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;