rs942518

chr9-114510578-G-A

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	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

Gnomad4 AFR AF: 0.419

Gnomad4 AMR AF: 0.732

Gnomad4 ASJ AF: 0.813

Gnomad4 EAS AF: 0.738

Gnomad4 SAS AF: 0.764

Gnomad4 FIN AF: 0.951

Gnomad4 NFE AF: 0.907

Gnomad4 OTH AF: 0.770

Alfa AF: 0.877 Hom.: 117553

Bravo AF: 0.711

Asia WGS AF: 0.757 AC: 2633 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.31
Cadd	Benign	14
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs942518; hg19: chr9-117272858;