rs7098387

chr10-20334544-A-Cchr10-20334544-A-T

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 0.129 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.112

Gnomad4 AMR AF: 0.106

Gnomad4 ASJ AF: 0.0447

Gnomad4 EAS AF: 0.106

Gnomad4 SAS AF: 0.0634

Gnomad4 FIN AF: 0.295

Gnomad4 NFE AF: 0.129

Gnomad4 OTH AF: 0.0917

Alfa AF: 0.117 Hom.: 1565

Bravo AF: 0.113

Asia WGS AF: 0.0710 AC: 245 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	1.0
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7098387; hg19: chr10-20623473;