10-122345409-A-G

Variant names:

• chr10-122345409-A-G
• rs6585818

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 0.846 in 152,186 control chromosomes in the GnomAD database, including 54,760 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 0.85 (54760 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.49
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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: 0.846 AC: 128582 AN: 152068 Hom.: 54708 Cov.: 32

Gnomad AFR AF: 0.919

Gnomad AMI AF: 0.757

Gnomad AMR AF: 0.847

Gnomad ASJ AF: 0.818

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.956

Gnomad FIN AF: 0.823

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.788

Gnomad OTH AF: 0.821

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

GnomAD4 genome AF: 0.846 AC: 128692 AN: 152186 Hom.: 54760 Cov.: 32 AF XY: 0.850 AC XY: 63268 AN XY: 74404

African (AFR) AF: 0.919 AC: 38164 AN: 41534

American (AMR) AF: 0.847 AC: 12953 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.818 AC: 2837 AN: 3470

East Asian (EAS) AF: 0.999 AC: 5179 AN: 5184

South Asian (SAS) AF: 0.956 AC: 4596 AN: 4808

European-Finnish (FIN) AF: 0.823 AC: 8708 AN: 10576

Middle Eastern (MID) AF: 0.861 AC: 253 AN: 294

European-Non Finnish (NFE) AF: 0.788 AC: 53575 AN: 68006

Other (OTH) AF: 0.823 AC: 1737 AN: 2110

Alfa AF: 0.803 Hom.: 21283

Bravo AF: 0.851

Asia WGS AF: 0.968 AC: 3365 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.0020
DANN	Benign	0.15
PhyloP100		-3.5

Splicing

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

Other links and lift over

dbSNP: rs6585818; hg19: chr10-124104924;