chr9-114510578-G-A

Variant names:

• chr9-114510578-G-A
• rs942518

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.744 in 152,124 control chromosomes in the GnomAD database, including 45,597 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 0.74 (45597 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.368
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.31).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.901 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: 0.745 AC: 113185 AN: 152006 Hom.: 45601 Cov.: 32

Gnomad AFR AF: 0.419

Gnomad AMI AF: 0.769

Gnomad AMR AF: 0.732

Gnomad ASJ AF: 0.813

Gnomad EAS AF: 0.739

Gnomad SAS AF: 0.764

Gnomad FIN AF: 0.951

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.907

Gnomad OTH AF: 0.770

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

GnomAD4 genome AF: 0.744 AC: 113196 AN: 152124 Hom.: 45597 Cov.: 32 AF XY: 0.745 AC XY: 55445 AN XY: 74400

African (AFR) AF: 0.419 AC: 17344 AN: 41436

American (AMR) AF: 0.732 AC: 11183 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.813 AC: 2820 AN: 3470

East Asian (EAS) AF: 0.738 AC: 3818 AN: 5170

South Asian (SAS) AF: 0.764 AC: 3686 AN: 4822

European-Finnish (FIN) AF: 0.951 AC: 10103 AN: 10626

Middle Eastern (MID) AF: 0.782 AC: 230 AN: 294

European-Non Finnish (NFE) AF: 0.907 AC: 61684 AN: 68006

Other (OTH) AF: 0.770 AC: 1627 AN: 2114

Alfa AF: 0.855 Hom.: 241764

Bravo AF: 0.711

Asia WGS AF: 0.757 AC: 2633 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.31
CADD	Benign	14
DANN	Benign	0.74
PhyloP100		0.37

Splicing

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

Other links and lift over

dbSNP: rs942518; hg19: chr9-117272858;