rs10757878

chr9-29504222-A-G

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 0.656 in 152,120 control chromosomes in the GnomAD database, including 32,993 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 0.66 (32993 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.248

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.819 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: 0.655 AC: 99619 AN: 152002 Hom.: 32955 Cov.: 33

Gnomad AFR AF: 0.687

Gnomad AMI AF: 0.446

Gnomad AMR AF: 0.712

Gnomad ASJ AF: 0.551

Gnomad EAS AF: 0.840

Gnomad SAS AF: 0.529

Gnomad FIN AF: 0.659

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.626

Gnomad OTH AF: 0.639

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

GnomAD4 genome AF: 0.656 AC: 99716 AN: 152120 Hom.: 32993 Cov.: 33 AF XY: 0.657 AC XY: 48849 AN XY: 74370

Gnomad4 AFR AF: 0.688

Gnomad4 AMR AF: 0.712

Gnomad4 ASJ AF: 0.551

Gnomad4 EAS AF: 0.840

Gnomad4 SAS AF: 0.530

Gnomad4 FIN AF: 0.659

Gnomad4 NFE AF: 0.626

Gnomad4 OTH AF: 0.640

Alfa AF: 0.639 Hom.: 6303

Bravo AF: 0.664

Asia WGS AF: 0.692 AC: 2404 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	0.93
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10757878; hg19: chr9-29504220;