rs10512064

chr9-77161416-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 0.112 in 152,210 control chromosomes in the GnomAD database, including 990 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 0.11 (990 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.246

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.119 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: 0.112 AC: 16960 AN: 152092 Hom.: 986 Cov.: 32

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.0658

Gnomad AMR AF: 0.0846

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.0366

Gnomad SAS AF: 0.0962

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.112 AC: 16978 AN: 152210 Hom.: 990 Cov.: 32 AF XY: 0.110 AC XY: 8189 AN XY: 74428

Gnomad4 AFR AF: 0.114

Gnomad4 AMR AF: 0.0845

Gnomad4 ASJ AF: 0.116

Gnomad4 EAS AF: 0.0369

Gnomad4 SAS AF: 0.0961

Gnomad4 FIN AF: 0.126

Gnomad4 NFE AF: 0.121

Gnomad4 OTH AF: 0.106

Alfa AF: 0.116 Hom.: 1388

Bravo AF: 0.108

Asia WGS AF: 0.0680 AC: 236 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	3.6
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10512064; hg19: chr9-79776332;