rs10120372

Variant names:

• chr9-105678261-T-C
• rs10120372

Your query was ambiguous. Multiple possible variants found:

• chr9-105678261-T-C
• chr9-105678261-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 0.1 in 152,170 control chromosomes in the GnomAD database, including 983 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 0.10 (983 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.330

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.175 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.100 AC: 15235 AN: 152052 Hom.: 986 Cov.: 32

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.0462

Gnomad AMR AF: 0.0654

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.0604

Gnomad OTH AF: 0.0924

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

GnomAD4 genome AF: 0.100 AC: 15243 AN: 152170 Hom.: 983 Cov.: 32 AF XY: 0.102 AC XY: 7603 AN XY: 74404

Gnomad4 AFR AF: 0.179

Gnomad4 AMR AF: 0.0654

Gnomad4 ASJ AF: 0.151

Gnomad4 EAS AF: 0.00154

Gnomad4 SAS AF: 0.136

Gnomad4 FIN AF: 0.118

Gnomad4 NFE AF: 0.0604

Gnomad4 OTH AF: 0.0919

Alfa AF: 0.0658 Hom.: 507

Bravo AF: 0.0980

Asia WGS AF: 0.0790 AC: 275 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.3
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10120372; hg19: chr9-108440542;