rs7898880

chr10-5995590-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 0.157 in 152,176 control chromosomes in the GnomAD database, including 2,486 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 0.16 (2486 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.769

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.23 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: 0.157 AC: 23864 AN: 152058 Hom.: 2485 Cov.: 32

Gnomad AFR AF: 0.0450

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.0110

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.157 AC: 23856 AN: 152176 Hom.: 2486 Cov.: 32 AF XY: 0.151 AC XY: 11264 AN XY: 74388

Gnomad4 AFR AF: 0.0449

Gnomad4 AMR AF: 0.151

Gnomad4 ASJ AF: 0.266

Gnomad4 EAS AF: 0.0110

Gnomad4 SAS AF: 0.118

Gnomad4 FIN AF: 0.136

Gnomad4 NFE AF: 0.233

Gnomad4 OTH AF: 0.184

Alfa AF: 0.222 Hom.: 7788

Bravo AF: 0.154

Asia WGS AF: 0.0670 AC: 232 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	3.9
Dann	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7898880; hg19: chr10-6037553;