11-114019986-A-G

Variant names:

• chr11-114019986-A-G
• rs2085421
• ENST00000770045.1:n.226-15276A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000770045.1(ENSG00000300211):​n.226-15276A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.569 in 152,072 control chromosomes in the GnomAD database, including 24,873 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 0.57 (24873 hom., cov: 33)
• Consequence: ENSG00000300211 ENST00000770045.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.35
• Publications: 2 publications found

Genes affected

ENSG00000300211 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.611 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000300211	ENST00000770045.1	n.226-15276A>G		intron_variant	Intron 2 of 3
ENSG00000300211	ENST00000770046.1	n.140+4493A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.569 AC: 86449 AN: 151954 Hom.: 24877 Cov.: 33

Gnomad AFR AF: 0.503

Gnomad AMI AF: 0.595

Gnomad AMR AF: 0.502

Gnomad ASJ AF: 0.604

Gnomad EAS AF: 0.532

Gnomad SAS AF: 0.565

Gnomad FIN AF: 0.631

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.616

Gnomad OTH AF: 0.550

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

GnomAD4 genome AF: 0.569 AC: 86470 AN: 152072 Hom.: 24873 Cov.: 33 AF XY: 0.567 AC XY: 42146 AN XY: 74318

African (AFR) AF: 0.502 AC: 20819 AN: 41446

American (AMR) AF: 0.501 AC: 7663 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.604 AC: 2097 AN: 3470

East Asian (EAS) AF: 0.531 AC: 2749 AN: 5174

South Asian (SAS) AF: 0.565 AC: 2725 AN: 4824

European-Finnish (FIN) AF: 0.631 AC: 6672 AN: 10566

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.616 AC: 41866 AN: 67978

Other (OTH) AF: 0.550 AC: 1162 AN: 2114

Alfa AF: 0.595 Hom.: 39713

Bravo AF: 0.555

Asia WGS AF: 0.524 AC: 1825 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.5
DANN	Benign	0.57
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs2085421; hg19: chr11-113890708;