rs10511429

chr9-1162143-G-Achr9-1162143-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;