rs11604758

Variant names:

• chr11-124851107-G-A
• rs11604758

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 0.619 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
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.642 AC: 26518 AN: 41294

American (AMR) AF: 0.570 AC: 8691 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.671 AC: 2329 AN: 3470

East Asian (EAS) AF: 0.301 AC: 1551 AN: 5152

South Asian (SAS) AF: 0.664 AC: 3184 AN: 4796

European-Finnish (FIN) AF: 0.696 AC: 7251 AN: 10420

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.620 AC: 42105 AN: 67884

Other (OTH) AF: 0.631 AC: 1332 AN: 2112

Alfa AF: 0.615 Hom.: 98292

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
PhyloP100		-0.035

Splicing

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

Other links and lift over

dbSNP: rs11604758; hg19: chr11-124721003;