11-18527334-A-G

Position:

• chr11-18527334-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000690266.2(ENSG00000289499):​n.378A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.884 in 154,008 control chromosomes in the GnomAD database, including 60,185 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 0.88 (59466 hom., cov: 31)
  • Exomes 𝑓: 0.89 (719 hom.)
• Consequence: ENSG00000289499 ENST00000690266.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.98

Genes affected

ENSG00000289499 (HGNC:):

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 (EAS) allele frequency at 95% confidence interval = 0.911 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.18527334A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000289499	ENST00000690266.2	n.378A>G		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.884 AC: 134402 AN: 152078 Hom.: 59415 Cov.: 31

Gnomad AFR AF: 0.859

Gnomad AMI AF: 0.906

Gnomad AMR AF: 0.883

Gnomad ASJ AF: 0.901

Gnomad EAS AF: 0.932

Gnomad SAS AF: 0.892

Gnomad FIN AF: 0.927

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.886

Gnomad OTH AF: 0.897

GnomAD4 exome AF: 0.887 AC: 1607 AN: 1812 Hom.: 719 AF XY: 0.888 AC XY: 927 AN XY: 1044

Gnomad4 AFR exome AF: 0.808

Gnomad4 AMR exome AF: 0.920

Gnomad4 ASJ exome AF: 0.861

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 0.884

Gnomad4 FIN exome AF: 0.861

Gnomad4 NFE exome AF: 0.881

Gnomad4 OTH exome AF: 0.931

GnomAD4 genome AF: 0.884 AC: 134512 AN: 152196 Hom.: 59466 Cov.: 31 AF XY: 0.885 AC XY: 65881 AN XY: 74406

Gnomad4 AFR AF: 0.859

Gnomad4 AMR AF: 0.883

Gnomad4 ASJ AF: 0.901

Gnomad4 EAS AF: 0.933

Gnomad4 SAS AF: 0.892

Gnomad4 FIN AF: 0.927

Gnomad4 NFE AF: 0.886

Gnomad4 OTH AF: 0.898

Alfa AF: 0.884 Hom.: 7944

Bravo AF: 0.881

Asia WGS AF: 0.928 AC: 3226 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	0.63
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1857909; hg19: chr11-18548881;