rs7098387

Variant names:

• chr10-20334544-A-C
• rs7098387

Your query was ambiguous. Multiple possible variants found:

• chr10-20334544-A-C
• chr10-20334544-A-T

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 0.129 in 151,168 control chromosomes in the GnomAD database, including 1,514 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 0.13 (1514 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0690
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.127 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19422 AN: 151050 Hom.: 1513 Cov.: 29

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.0447

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.0638

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.0927

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

GnomAD4 genome AF: 0.129 AC: 19442 AN: 151168 Hom.: 1514 Cov.: 29 AF XY: 0.135 AC XY: 9927 AN XY: 73784

African (AFR) AF: 0.112 AC: 4616 AN: 41154

American (AMR) AF: 0.106 AC: 1602 AN: 15084

Ashkenazi Jewish (ASJ) AF: 0.0447 AC: 155 AN: 3466

East Asian (EAS) AF: 0.106 AC: 548 AN: 5150

South Asian (SAS) AF: 0.0634 AC: 300 AN: 4730

European-Finnish (FIN) AF: 0.295 AC: 3068 AN: 10404

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.129 AC: 8773 AN: 67882

Other (OTH) AF: 0.0917 AC: 192 AN: 2094

Alfa AF: 0.117 Hom.: 2087

Bravo AF: 0.113

Asia WGS AF: 0.0710 AC: 245 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.0
DANN	Benign	0.63
PhyloP100		-0.069

Splicing

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

Other links and lift over

dbSNP: rs7098387; hg19: chr10-20623473;