9-96789704-A-G

Variant names:

• chr9-96789704-A-G
• rs10119556

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 0.143 in 152,078 control chromosomes in the GnomAD database, including 3,528 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 (3528 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.381 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21658 AN: 151960 Hom.: 3495 Cov.: 32

Gnomad AFR AF: 0.385

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0684

Gnomad ASJ AF: 0.0245

Gnomad EAS AF: 0.338

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.0923

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0165

Gnomad OTH AF: 0.0976

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

GnomAD4 genome AF: 0.143 AC: 21730 AN: 152078 Hom.: 3528 Cov.: 32 AF XY: 0.146 AC XY: 10884 AN XY: 74326

African (AFR) AF: 0.386 AC: 15983 AN: 41432

American (AMR) AF: 0.0682 AC: 1042 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0245 AC: 85 AN: 3470

East Asian (EAS) AF: 0.338 AC: 1740 AN: 5154

South Asian (SAS) AF: 0.113 AC: 546 AN: 4820

European-Finnish (FIN) AF: 0.0923 AC: 977 AN: 10586

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0165 AC: 1120 AN: 68010

Other (OTH) AF: 0.0966 AC: 204 AN: 2112

Alfa AF: 0.0942 Hom.: 391

Bravo AF: 0.153

Asia WGS AF: 0.195 AC: 677 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.3
DANN	Benign	0.33
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs10119556; hg19: chr9-99551986;