rs4437724

chr9-113346815-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.166 in 151,704 control chromosomes in the GnomAD database, including 2,913 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 0.17 (2913 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.285

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.323 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: 0.166 AC: 25111 AN: 151586 Hom.: 2904 Cov.: 31

Gnomad AFR AF: 0.328

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.0346

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.0569

Gnomad MID AF: 0.122

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.145

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

GnomAD4 genome AF: 0.166 AC: 25139 AN: 151704 Hom.: 2913 Cov.: 31 AF XY: 0.163 AC XY: 12087 AN XY: 74148

Gnomad4 AFR AF: 0.328

Gnomad4 AMR AF: 0.101

Gnomad4 ASJ AF: 0.137

Gnomad4 EAS AF: 0.0341

Gnomad4 SAS AF: 0.187

Gnomad4 FIN AF: 0.0569

Gnomad4 NFE AF: 0.109

Gnomad4 OTH AF: 0.143

Alfa AF: 0.129 Hom.: 744

Bravo AF: 0.172

Asia WGS AF: 0.120 AC: 417 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.92
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4437724; hg19: chr9-116109095;