9-25612706-T-G

Variant names:

• chr9-25612706-T-G
• rs10511761

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 0.516 in 152,048 control chromosomes in the GnomAD database, including 21,266 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 0.52 (21266 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.847

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.622 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: 0.516 AC: 78404 AN: 151932 Hom.: 21266 Cov.: 32

Gnomad AFR AF: 0.335

Gnomad AMI AF: 0.724

Gnomad AMR AF: 0.632

Gnomad ASJ AF: 0.571

Gnomad EAS AF: 0.552

Gnomad SAS AF: 0.540

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.586

Gnomad OTH AF: 0.533

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

GnomAD4 genome AF: 0.516 AC: 78426 AN: 152048 Hom.: 21266 Cov.: 32 AF XY: 0.516 AC XY: 38330 AN XY: 74328

Gnomad4 AFR AF: 0.334

Gnomad4 AMR AF: 0.632

Gnomad4 ASJ AF: 0.571

Gnomad4 EAS AF: 0.551

Gnomad4 SAS AF: 0.538

Gnomad4 FIN AF: 0.539

Gnomad4 NFE AF: 0.586

Gnomad4 OTH AF: 0.533

Alfa AF: 0.571 Hom.: 33025

Bravo AF: 0.518

Asia WGS AF: 0.541 AC: 1879 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	17
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10511761; hg19: chr9-25612704;