rs10512289

Positions:

• chr9-101748176-T-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 0.0706 in 152,040 control chromosomes in the GnomAD database, including 804 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 0.071 (804 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.402

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.189 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0705 AC: 10716 AN: 151922 Hom.: 802 Cov.: 32

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0400

Gnomad ASJ AF: 0.0173

Gnomad EAS AF: 0.0143

Gnomad SAS AF: 0.0294

Gnomad FIN AF: 0.0278

Gnomad MID AF: 0.0732

Gnomad NFE AF: 0.0210

Gnomad OTH AF: 0.0595

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

GnomAD4 genome AF: 0.0706 AC: 10739 AN: 152040 Hom.: 804 Cov.: 32 AF XY: 0.0700 AC XY: 5202 AN XY: 74346

Gnomad4 AFR AF: 0.192

Gnomad4 AMR AF: 0.0399

Gnomad4 ASJ AF: 0.0173

Gnomad4 EAS AF: 0.0143

Gnomad4 SAS AF: 0.0298

Gnomad4 FIN AF: 0.0278

Gnomad4 NFE AF: 0.0210

Gnomad4 OTH AF: 0.0641

Alfa AF: 0.0557 Hom.: 133

Bravo AF: 0.0759

Asia WGS AF: 0.0400 AC: 140 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.78
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10512289; hg19: chr9-104510458;