chr11-56408195-C-G

Position:

• chr11-56408195-C-G

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 0.747 in 152,056 control chromosomes in the GnomAD database, including 42,453 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 0.75 (42453 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.43

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.789 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.56408195C>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.747 AC: 113444 AN: 151938 Hom.: 42414 Cov.: 32

Gnomad AFR AF: 0.765

Gnomad AMI AF: 0.737

Gnomad AMR AF: 0.800

Gnomad ASJ AF: 0.778

Gnomad EAS AF: 0.772

Gnomad SAS AF: 0.800

Gnomad FIN AF: 0.708

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.722

Gnomad OTH AF: 0.773

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

GnomAD4 genome AF: 0.747 AC: 113537 AN: 152056 Hom.: 42453 Cov.: 32 AF XY: 0.747 AC XY: 55488 AN XY: 74314

Gnomad4 AFR AF: 0.764

Gnomad4 AMR AF: 0.801

Gnomad4 ASJ AF: 0.778

Gnomad4 EAS AF: 0.772

Gnomad4 SAS AF: 0.801

Gnomad4 FIN AF: 0.708

Gnomad4 NFE AF: 0.722

Gnomad4 OTH AF: 0.777

Alfa AF: 0.720 Hom.: 19141

Bravo AF: 0.759

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.018
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1945213; hg19: chr11-56175671;