rs11604758

Variant names:

• chr11-124851107-G-A
• rs11604758

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 0.619 in 151,568 control chromosomes in the GnomAD database, including 29,414 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 0.62 (29414 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0350

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.645 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: 0.618 AC: 93661 AN: 151450 Hom.: 29373 Cov.: 30

Gnomad AFR AF: 0.642

Gnomad AMI AF: 0.670

Gnomad AMR AF: 0.571

Gnomad ASJ AF: 0.671

Gnomad EAS AF: 0.302

Gnomad SAS AF: 0.663

Gnomad FIN AF: 0.696

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.620

Gnomad OTH AF: 0.629

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

GnomAD4 genome AF: 0.619 AC: 93757 AN: 151568 Hom.: 29414 Cov.: 30 AF XY: 0.621 AC XY: 45946 AN XY: 74014

Gnomad4 AFR AF: 0.642

Gnomad4 AMR AF: 0.570

Gnomad4 ASJ AF: 0.671

Gnomad4 EAS AF: 0.301

Gnomad4 SAS AF: 0.664

Gnomad4 FIN AF: 0.696

Gnomad4 NFE AF: 0.620

Gnomad4 OTH AF: 0.631

Alfa AF: 0.616 Hom.: 60080

Bravo AF: 0.604

Asia WGS AF: 0.542 AC: 1888 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	2.7
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11604758; hg19: chr11-124721003;