rs7902878

Variant names:

• chr10-122529208-G-A
• rs7902878

Your query was ambiguous. Multiple possible variants found:

• chr10-122529208-G-A
• chr10-122529208-G-C

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 0.244 in 151,676 control chromosomes in the GnomAD database, including 5,042 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 0.24 (5042 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.697

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.299 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: 0.245 AC: 37078 AN: 151556 Hom.: 5040 Cov.: 31

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.373

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.234

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

GnomAD4 genome AF: 0.244 AC: 37075 AN: 151676 Hom.: 5042 Cov.: 31 AF XY: 0.246 AC XY: 18193 AN XY: 74044

Gnomad4 AFR AF: 0.134

Gnomad4 AMR AF: 0.223

Gnomad4 ASJ AF: 0.236

Gnomad4 EAS AF: 0.205

Gnomad4 SAS AF: 0.189

Gnomad4 FIN AF: 0.373

Gnomad4 NFE AF: 0.303

Gnomad4 OTH AF: 0.234

Alfa AF: 0.282 Hom.: 11214

Bravo AF: 0.226

Asia WGS AF: 0.194 AC: 675 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.52
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7902878; hg19: chr10-124288724;