10-122364790-A-G

Variant names:

• chr10-122364790-A-G
• rs1998345

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.873 AC: 36270 AN: 41544

American (AMR) AF: 0.687 AC: 10511 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.668 AC: 2320 AN: 3472

East Asian (EAS) AF: 0.701 AC: 3619 AN: 5162

South Asian (SAS) AF: 0.632 AC: 3052 AN: 4826

European-Finnish (FIN) AF: 0.632 AC: 6678 AN: 10568

Middle Eastern (MID) AF: 0.673 AC: 198 AN: 294

European-Non Finnish (NFE) AF: 0.649 AC: 44144 AN: 67992

Other (OTH) AF: 0.702 AC: 1479 AN: 2108

Alfa AF: 0.669 Hom.: 51670

Bravo AF: 0.730

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.14
DANN	Benign	0.67
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs1998345; hg19: chr10-124124306;