rs11227638

Positions:

• chr11-56252109-A-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 0.117 in 652,830 control chromosomes in the GnomAD database, including 5,018 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 0.11 (1002 hom., cov: 32)
  • Exomes 𝑓: 0.12 (4016 hom.)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.435

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.132 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.56252109A>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.105 AC: 15984 AN: 151906 Hom.: 1003 Cov.: 32

Gnomad AFR AF: 0.0578

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.0929

Gnomad ASJ AF: 0.0869

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.199

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.0856

GnomAD4 exome AF: 0.121 AC: 60417 AN: 500806 Hom.: 4016 AF XY: 0.121 AC XY: 31203 AN XY: 258180

Gnomad4 AFR exome AF: 0.0577

Gnomad4 AMR exome AF: 0.104

Gnomad4 ASJ exome AF: 0.0835

Gnomad4 EAS exome AF: 0.129

Gnomad4 SAS exome AF: 0.123

Gnomad4 FIN exome AF: 0.178

Gnomad4 NFE exome AF: 0.119

Gnomad4 OTH exome AF: 0.109

GnomAD4 genome AF: 0.105 AC: 15978 AN: 152024 Hom.: 1002 Cov.: 32 AF XY: 0.109 AC XY: 8077 AN XY: 74320

Gnomad4 AFR AF: 0.0578

Gnomad4 AMR AF: 0.0927

Gnomad4 ASJ AF: 0.0869

Gnomad4 EAS AF: 0.141

Gnomad4 SAS AF: 0.121

Gnomad4 FIN AF: 0.199

Gnomad4 NFE AF: 0.120

Gnomad4 OTH AF: 0.0838

Alfa AF: 0.109 Hom.: 133

Bravo AF: 0.0963

Asia WGS AF: 0.108 AC: 374 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.0
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11227638; hg19: chr11-56019585;