rs581133

Positions:

• chr11-60114833-A-G
• chr11-60114833-A-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 0.391 in 152,024 control chromosomes in the GnomAD database, including 11,999 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 0.39 (11999 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.574

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 (SAS) allele frequency at 95% confidence interval = 0.529 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: 0.391 AC: 59339 AN: 151906 Hom.: 11991 Cov.: 32

Gnomad AFR AF: 0.320

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.461

Gnomad EAS AF: 0.377

Gnomad SAS AF: 0.546

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.442

Gnomad OTH AF: 0.430

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

GnomAD4 genome AF: 0.391 AC: 59370 AN: 152024 Hom.: 11999 Cov.: 32 AF XY: 0.387 AC XY: 28730 AN XY: 74326

Gnomad4 AFR AF: 0.320

Gnomad4 AMR AF: 0.339

Gnomad4 ASJ AF: 0.461

Gnomad4 EAS AF: 0.377

Gnomad4 SAS AF: 0.547

Gnomad4 FIN AF: 0.307

Gnomad4 NFE AF: 0.442

Gnomad4 OTH AF: 0.429

Alfa AF: 0.431 Hom.: 6710

Bravo AF: 0.386

Asia WGS AF: 0.461 AC: 1603 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	0.77
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs581133; hg19: chr11-59882306;