rs4754011

chr11-97071393-G-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 0.203 in 151,432 control chromosomes in the GnomAD database, including 3,388 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 0.20 (3388 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.455 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: 0.203 AC: 30766 AN: 151312 Hom.: 3391 Cov.: 31

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.472

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.248

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.203 AC: 30791 AN: 151432 Hom.: 3388 Cov.: 31 AF XY: 0.208 AC XY: 15359 AN XY: 73954

Gnomad4 AFR AF: 0.173

Gnomad4 AMR AF: 0.249

Gnomad4 ASJ AF: 0.207

Gnomad4 EAS AF: 0.471

Gnomad4 SAS AF: 0.279

Gnomad4 FIN AF: 0.159

Gnomad4 NFE AF: 0.192

Gnomad4 OTH AF: 0.205

Alfa AF: 0.196 Hom.: 3037

Bravo AF: 0.207

Asia WGS AF: 0.356 AC: 1235 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	4.5
Dann	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4754011; hg19: chr11-96942393;