rs7897194

Variant names:

• chr10-20503405-G-A
• rs7897194

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;