9-105678261-T-C

Variant names:

• chr9-105678261-T-C
• rs10120372

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.179 AC: 7417 AN: 41482

American (AMR) AF: 0.0654 AC: 1000 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.151 AC: 523 AN: 3470

East Asian (EAS) AF: 0.00154 AC: 8 AN: 5182

South Asian (SAS) AF: 0.136 AC: 656 AN: 4820

European-Finnish (FIN) AF: 0.118 AC: 1247 AN: 10600

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.0604 AC: 4110 AN: 68014

Other (OTH) AF: 0.0919 AC: 194 AN: 2110

Alfa AF: 0.0752 Hom.: 1218

Bravo AF: 0.0980

Asia WGS AF: 0.0790 AC: 275 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.3
DANN	Benign	0.81
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs10120372; hg19: chr9-108440542;