rs3924745

Variant names:

• chr11-24201455-G-A
• rs3924745

Your query was ambiguous. Multiple possible variants found:

• chr11-24201455-G-A
• chr11-24201455-G-T

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 0.309 in 150,616 control chromosomes in the GnomAD database, including 10,505 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 0.31 (10505 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.131

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 = 0.628 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.308 AC: 46433 AN: 150520 Hom.: 10467 Cov.: 30

Gnomad AFR AF: 0.633

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.238

Gnomad EAS AF: 0.306

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.299

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

GnomAD4 genome AF: 0.309 AC: 46528 AN: 150616 Hom.: 10505 Cov.: 30 AF XY: 0.307 AC XY: 22612 AN XY: 73564

Gnomad4 AFR AF: 0.634

Gnomad4 AMR AF: 0.284

Gnomad4 ASJ AF: 0.238

Gnomad4 EAS AF: 0.306

Gnomad4 SAS AF: 0.295

Gnomad4 FIN AF: 0.105

Gnomad4 NFE AF: 0.156

Gnomad4 OTH AF: 0.297

Alfa AF: 0.205 Hom.: 1707

Bravo AF: 0.333

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.27
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3924745; hg19: chr11-24223001;