rs11604821

Positions:

• chr11-69537369-G-A

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 0.475 in 152,200 control chromosomes in the GnomAD database, including 21,342 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 0.47 (21342 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00300

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.652 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.475 AC: 72234 AN: 152082 Hom.: 21346 Cov.: 33

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.701

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.516

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.505

Gnomad FIN AF: 0.766

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.657

Gnomad OTH AF: 0.470

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

GnomAD4 genome AF: 0.475 AC: 72231 AN: 152200 Hom.: 21342 Cov.: 33 AF XY: 0.476 AC XY: 35450 AN XY: 74416

Gnomad4 AFR AF: 0.142

Gnomad4 AMR AF: 0.410

Gnomad4 ASJ AF: 0.516

Gnomad4 EAS AF: 0.241

Gnomad4 SAS AF: 0.506

Gnomad4 FIN AF: 0.766

Gnomad4 NFE AF: 0.657

Gnomad4 OTH AF: 0.467

Alfa AF: 0.612 Hom.: 16958

Bravo AF: 0.432

Asia WGS AF: 0.375 AC: 1306 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.2
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11604821; hg19: chr11-69352137;