11-34538699-G-C

Position:

• chr11-34538699-G-C

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 0.172 in 152,086 control chromosomes in the GnomAD database, including 2,878 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 0.17 (2878 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.937

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.387 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.34538699G>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000255271	ENST00000527984.1	n.237-5533C>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.171 AC: 26046 AN: 151968 Hom.: 2854 Cov.: 31

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.0957

Gnomad EAS AF: 0.401

Gnomad SAS AF: 0.0896

Gnomad FIN AF: 0.0520

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.172 AC: 26119 AN: 152086 Hom.: 2878 Cov.: 31 AF XY: 0.169 AC XY: 12571 AN XY: 74366

Gnomad4 AFR AF: 0.290

Gnomad4 AMR AF: 0.147

Gnomad4 ASJ AF: 0.0957

Gnomad4 EAS AF: 0.402

Gnomad4 SAS AF: 0.0895

Gnomad4 FIN AF: 0.0520

Gnomad4 NFE AF: 0.117

Gnomad4 OTH AF: 0.178

Alfa AF: 0.0442 Hom.: 39

Bravo AF: 0.189

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.11
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs836126; hg19: chr11-34560246;