rs733601

Variant names:

• chr11-124844984-G-A
• rs733601

Your query was ambiguous. Multiple possible variants found:

• chr11-124844984-G-A
• chr11-124844984-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.254 in 152,112 control chromosomes in the GnomAD database, including 5,509 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 0.25 (5509 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.11
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.367 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: 0.254 AC: 38553 AN: 151994 Hom.: 5487 Cov.: 32

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.198

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.254 AC: 38632 AN: 152112 Hom.: 5509 Cov.: 32 AF XY: 0.258 AC XY: 19208 AN XY: 74344

African (AFR) AF: 0.372 AC: 15441 AN: 41490

American (AMR) AF: 0.298 AC: 4553 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.193 AC: 671 AN: 3470

East Asian (EAS) AF: 0.199 AC: 1026 AN: 5164

South Asian (SAS) AF: 0.278 AC: 1341 AN: 4822

European-Finnish (FIN) AF: 0.221 AC: 2337 AN: 10580

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.185 AC: 12567 AN: 67990

Other (OTH) AF: 0.221 AC: 467 AN: 2114

Alfa AF: 0.232 Hom.: 769

Bravo AF: 0.267

Asia WGS AF: 0.274 AC: 954 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.012
DANN	Benign	0.51
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs733601; hg19: chr11-124714880;