rs10985375

chr9-121787363-C-Achr9-121787363-C-Gchr9-121787363-C-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 0.14 in 151,974 control chromosomes in the GnomAD database, including 1,640 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 (1640 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.874

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 (EAS) allele frequency at 95% confidence interval = 0.203 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: 0.140 AC: 21302 AN: 151856 Hom.: 1644 Cov.: 29

Gnomad AFR AF: 0.0903

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.213

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.213

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.157

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

GnomAD4 genome AF: 0.140 AC: 21299 AN: 151974 Hom.: 1640 Cov.: 29 AF XY: 0.140 AC XY: 10421 AN XY: 74270

Gnomad4 AFR AF: 0.0902

Gnomad4 AMR AF: 0.153

Gnomad4 ASJ AF: 0.181

Gnomad4 EAS AF: 0.213

Gnomad4 SAS AF: 0.151

Gnomad4 FIN AF: 0.159

Gnomad4 NFE AF: 0.156

Gnomad4 OTH AF: 0.156

Alfa AF: 0.104 Hom.: 224

Bravo AF: 0.140

Asia WGS AF: 0.169 AC: 587 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	0.077
Dann	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10985375; hg19: chr9-124549642;