chr10-103469769-A-G

Variant names:

• chr10-103469769-A-G
• rs2986030

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 0.807 in 152,264 control chromosomes in the GnomAD database, including 49,828 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 0.81 (49828 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.532
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.889 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: 0.807 AC: 122713 AN: 152146 Hom.: 49775 Cov.: 34

Gnomad AFR AF: 0.871

Gnomad AMI AF: 0.681

Gnomad AMR AF: 0.841

Gnomad ASJ AF: 0.753

Gnomad EAS AF: 0.911

Gnomad SAS AF: 0.879

Gnomad FIN AF: 0.795

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.753

Gnomad OTH AF: 0.794

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

GnomAD4 genome AF: 0.807 AC: 122826 AN: 152264 Hom.: 49828 Cov.: 34 AF XY: 0.810 AC XY: 60330 AN XY: 74438

African (AFR) AF: 0.871 AC: 36186 AN: 41546

American (AMR) AF: 0.841 AC: 12866 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.753 AC: 2616 AN: 3472

East Asian (EAS) AF: 0.911 AC: 4712 AN: 5174

South Asian (SAS) AF: 0.879 AC: 4246 AN: 4828

European-Finnish (FIN) AF: 0.795 AC: 8440 AN: 10610

Middle Eastern (MID) AF: 0.759 AC: 223 AN: 294

European-Non Finnish (NFE) AF: 0.753 AC: 51233 AN: 68024

Other (OTH) AF: 0.796 AC: 1684 AN: 2116

Alfa AF: 0.778 Hom.: 5998

Bravo AF: 0.813

Asia WGS AF: 0.908 AC: 3158 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.5
DANN	Benign	0.48
PhyloP100		0.53

Splicing

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

Other links and lift over

dbSNP: rs2986030; hg19: chr10-105229526;