rs7950726

chr11-5204217-C-A

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 0.163 in 151,906 control chromosomes in the GnomAD database, including 2,419 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 0.16 (2419 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.267 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: 0.163 AC: 24699 AN: 151786 Hom.: 2409 Cov.: 32

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.0439

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.0879

Gnomad EAS AF: 0.0244

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.134

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.163 AC: 24734 AN: 151906 Hom.: 2419 Cov.: 32 AF XY: 0.162 AC XY: 12050 AN XY: 74248

Gnomad4 AFR AF: 0.271

Gnomad4 AMR AF: 0.114

Gnomad4 ASJ AF: 0.0879

Gnomad4 EAS AF: 0.0246

Gnomad4 SAS AF: 0.185

Gnomad4 FIN AF: 0.153

Gnomad4 NFE AF: 0.124

Gnomad4 OTH AF: 0.152

Alfa AF: 0.137 Hom.: 768

Bravo AF: 0.156

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	-1.0
Cadd	Benign	1.0
Dann	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7950726; hg19: chr11-5225447;