9-114756649-G-C

Variant names:

• chr9-114756649-G-C
• rs10982396

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 0.917 in 152,224 control chromosomes in the GnomAD database, including 64,123 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 0.92 (64123 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.917 AC: 139419 AN: 152106 Hom.: 64066 Cov.: 32

Gnomad AFR AF: 0.964

Gnomad AMI AF: 0.932

Gnomad AMR AF: 0.876

Gnomad ASJ AF: 0.933

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.977

Gnomad FIN AF: 0.951

Gnomad MID AF: 0.911

Gnomad NFE AF: 0.881

Gnomad OTH AF: 0.894

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

GnomAD4 genome AF: 0.917 AC: 139533 AN: 152224 Hom.: 64123 Cov.: 32 AF XY: 0.921 AC XY: 68537 AN XY: 74416

African (AFR) AF: 0.964 AC: 40041 AN: 41538

American (AMR) AF: 0.876 AC: 13388 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.933 AC: 3240 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5163 AN: 5168

South Asian (SAS) AF: 0.977 AC: 4711 AN: 4822

European-Finnish (FIN) AF: 0.951 AC: 10081 AN: 10602

Middle Eastern (MID) AF: 0.908 AC: 267 AN: 294

European-Non Finnish (NFE) AF: 0.881 AC: 59901 AN: 68022

Other (OTH) AF: 0.895 AC: 1891 AN: 2112

Alfa AF: 0.903 Hom.: 7711

Bravo AF: 0.912

Asia WGS AF: 0.980 AC: 3408 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.81
DANN	Benign	0.40
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs10982396; hg19: chr9-117518929; COSMIC: COSV60395578;