11-34478532-A-G

Variant names:

• chr11-34478532-A-G
• rs1535721

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 0.652 in 152,056 control chromosomes in the GnomAD database, including 35,075 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 0.65 (35075 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.904

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.786 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: 0.653 AC: 99155 AN: 151938 Hom.: 35070 Cov.: 31

Gnomad AFR AF: 0.369

Gnomad AMI AF: 0.880

Gnomad AMR AF: 0.697

Gnomad ASJ AF: 0.708

Gnomad EAS AF: 0.451

Gnomad SAS AF: 0.808

Gnomad FIN AF: 0.793

Gnomad MID AF: 0.571

Gnomad NFE AF: 0.792

Gnomad OTH AF: 0.662

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

GnomAD4 genome AF: 0.652 AC: 99187 AN: 152056 Hom.: 35075 Cov.: 31 AF XY: 0.656 AC XY: 48752 AN XY: 74324

Gnomad4 AFR AF: 0.369

Gnomad4 AMR AF: 0.697

Gnomad4 ASJ AF: 0.708

Gnomad4 EAS AF: 0.451

Gnomad4 SAS AF: 0.807

Gnomad4 FIN AF: 0.793

Gnomad4 NFE AF: 0.792

Gnomad4 OTH AF: 0.660

Alfa AF: 0.769 Hom.: 60157

Bravo AF: 0.629

Asia WGS AF: 0.613 AC: 2136 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	10
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1535721; hg19: chr11-34500079;