ENST00000690266.2:n.378A>G

Variant names:

• chr11-18527334-A-G
• rs1857909
• ENST00000690266.2:n.378A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

Genes affected

ENSG00000289499 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000690266.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000289499	ENST00000690266.2		n.378A>G		non_coding_transcript_exon	Exon 1 of 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

African (AFR) AF: 0.808 AC: 21 AN: 26

American (AMR) AF: 0.920 AC: 195 AN: 212

Ashkenazi Jewish (ASJ) AF: 0.861 AC: 31 AN: 36

East Asian (EAS) AF: 1.00 AC: 14 AN: 14

South Asian (SAS) AF: 0.884 AC: 465 AN: 526

European-Finnish (FIN) AF: 0.861 AC: 31 AN: 36

Middle Eastern (MID) AF: 0.500 AC: 1 AN: 2

European-Non Finnish (NFE) AF: 0.881 AC: 782 AN: 888

Other (OTH) AF: 0.931 AC: 67 AN: 72

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

African (AFR) AF: 0.859 AC: 35650 AN: 41488

American (AMR) AF: 0.883 AC: 13499 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.901 AC: 3128 AN: 3472

East Asian (EAS) AF: 0.933 AC: 4828 AN: 5176

South Asian (SAS) AF: 0.892 AC: 4306 AN: 4826

European-Finnish (FIN) AF: 0.927 AC: 9827 AN: 10600

Middle Eastern (MID) AF: 0.867 AC: 255 AN: 294

European-Non Finnish (NFE) AF: 0.886 AC: 60295 AN: 68020

Other (OTH) AF: 0.898 AC: 1898 AN: 2114

Alfa AF: 0.883 Hom.: 8239

Bravo AF: 0.881

Asia WGS AF: 0.928 AC: 3226 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.63
DANN	Benign	0.61
PhyloP100		-2.0
PromoterAI		-0.021	Neutral

Splicing

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

Other links and lift over

dbSNP: rs1857909; hg19: chr11-18548881;