rs7898880

Variant names:

• chr10-5995590-G-A
• rs7898880

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 0.157 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
• Publications: 13 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0449 AC: 1863 AN: 41530

American (AMR) AF: 0.151 AC: 2305 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.266 AC: 923 AN: 3466

East Asian (EAS) AF: 0.0110 AC: 57 AN: 5190

South Asian (SAS) AF: 0.118 AC: 569 AN: 4822

European-Finnish (FIN) AF: 0.136 AC: 1439 AN: 10592

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.233 AC: 15851 AN: 67986

Other (OTH) AF: 0.184 AC: 389 AN: 2110

Alfa AF: 0.211 Hom.: 14972

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
PhyloP100		0.77

Splicing

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

Other links and lift over

dbSNP: rs7898880; hg19: chr10-6037553;