rs9804317

Positions:

• chr10-128450662-T-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 0.138 in 152,158 control chromosomes in the GnomAD database, including 1,913 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 0.14 (1913 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.386 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: 0.138 AC: 20989 AN: 152040 Hom.: 1910 Cov.: 33

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.0866

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.401

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.0673

Gnomad MID AF: 0.156

Gnomad NFE AF: 0.0827

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.138 AC: 20998 AN: 152158 Hom.: 1913 Cov.: 33 AF XY: 0.143 AC XY: 10615 AN XY: 74404

Gnomad4 AFR AF: 0.203

Gnomad4 AMR AF: 0.144

Gnomad4 ASJ AF: 0.108

Gnomad4 EAS AF: 0.400

Gnomad4 SAS AF: 0.248

Gnomad4 FIN AF: 0.0673

Gnomad4 NFE AF: 0.0827

Gnomad4 OTH AF: 0.132

Alfa AF: 0.100 Hom.: 2321

Bravo AF: 0.148

Asia WGS AF: 0.313 AC: 1088 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.32
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9804317; hg19: chr10-130248926;