rs7897194

chr10-20503405-G-A

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 0.171 in 152,076 control chromosomes in the GnomAD database, including 2,747 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 0.17 (2747 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.405

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.289 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: 0.171 AC: 26001 AN: 151958 Hom.: 2747 Cov.: 32

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.0844

Gnomad EAS AF: 0.0253

Gnomad SAS AF: 0.0896

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.105

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.171 AC: 26025 AN: 152076 Hom.: 2747 Cov.: 32 AF XY: 0.170 AC XY: 12641 AN XY: 74334

Gnomad4 AFR AF: 0.293

Gnomad4 AMR AF: 0.127

Gnomad4 ASJ AF: 0.0844

Gnomad4 EAS AF: 0.0254

Gnomad4 SAS AF: 0.0891

Gnomad4 FIN AF: 0.176

Gnomad4 NFE AF: 0.129

Gnomad4 OTH AF: 0.133

Alfa AF: 0.143 Hom.: 972

Bravo AF: 0.173

Asia WGS AF: 0.0550 AC: 194 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	3.6
Dann	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7897194; hg19: chr10-20792334;