rs10511429

Variant names:

• chr9-1162143-G-A
• rs10511429

Your query was ambiguous. Multiple possible variants found:

• chr9-1162143-G-A
• chr9-1162143-G-T

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 151,976 control chromosomes in the GnomAD database, including 20,871 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 (20871 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.451

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.737 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: 78312 AN: 151858 Hom.: 20839 Cov.: 32

Gnomad AFR AF: 0.582

Gnomad AMI AF: 0.393

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.756

Gnomad SAS AF: 0.580

Gnomad FIN AF: 0.614

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.501

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

GnomAD4 genome AF: 0.516 AC: 78397 AN: 151976 Hom.: 20871 Cov.: 32 AF XY: 0.525 AC XY: 39028 AN XY: 74286

Gnomad4 AFR AF: 0.582

Gnomad4 AMR AF: 0.550

Gnomad4 ASJ AF: 0.381

Gnomad4 EAS AF: 0.756

Gnomad4 SAS AF: 0.580

Gnomad4 FIN AF: 0.614

Gnomad4 NFE AF: 0.439

Gnomad4 OTH AF: 0.506

Alfa AF: 0.469 Hom.: 3404

Bravo AF: 0.514

Asia WGS AF: 0.692 AC: 2407 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	11
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10511429; hg19: chr9-1162143;