11-4521622-C-T

Position:

• chr11-4521622-C-T

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 0.0803 in 151,782 control chromosomes in the GnomAD database, including 1,068 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 0.080 (1068 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.276

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.201 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.4521622C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0801 AC: 12142 AN: 151664 Hom.: 1063 Cov.: 32

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.0439

Gnomad AMR AF: 0.0455

Gnomad ASJ AF: 0.0566

Gnomad EAS AF: 0.0441

Gnomad SAS AF: 0.0203

Gnomad FIN AF: 0.0110

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0324

Gnomad OTH AF: 0.0714

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

GnomAD4 genome AF: 0.0803 AC: 12183 AN: 151782 Hom.: 1068 Cov.: 32 AF XY: 0.0778 AC XY: 5769 AN XY: 74170

Gnomad4 AFR AF: 0.205

Gnomad4 AMR AF: 0.0454

Gnomad4 ASJ AF: 0.0566

Gnomad4 EAS AF: 0.0438

Gnomad4 SAS AF: 0.0205

Gnomad4 FIN AF: 0.0110

Gnomad4 NFE AF: 0.0324

Gnomad4 OTH AF: 0.0731

Alfa AF: 0.00707 Hom.: 5

Bravo AF: 0.0878

Asia WGS AF: 0.0570 AC: 198 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.7
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10500605; hg19: chr11-4542852;