11-87576547-G-A

Variant names:

• chr11-87576547-G-A
• rs2226844
• XR_001748316.2:n.389+23178G>A

Variant summary

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

The XR_001748316.2(LOC107984361):​n.389+23178G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.633 in 151,944 control chromosomes in the GnomAD database, including 30,895 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 0.63 (30895 hom., cov: 32)
• Consequence: LOC107984361 XR_001748316.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0810
• Publications: 1 publications found

Genes affected

LOC107984361 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.69 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.633 AC: 96079 AN: 151824 Hom.: 30855 Cov.: 32

Gnomad AFR AF: 0.696

Gnomad AMI AF: 0.675

Gnomad AMR AF: 0.634

Gnomad ASJ AF: 0.766

Gnomad EAS AF: 0.349

Gnomad SAS AF: 0.523

Gnomad FIN AF: 0.486

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.638

Gnomad OTH AF: 0.656

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

GnomAD4 genome AF: 0.633 AC: 96175 AN: 151944 Hom.: 30895 Cov.: 32 AF XY: 0.624 AC XY: 46351 AN XY: 74258

African (AFR) AF: 0.696 AC: 28859 AN: 41444

American (AMR) AF: 0.633 AC: 9666 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.766 AC: 2657 AN: 3470

East Asian (EAS) AF: 0.349 AC: 1791 AN: 5138

South Asian (SAS) AF: 0.522 AC: 2515 AN: 4820

European-Finnish (FIN) AF: 0.486 AC: 5132 AN: 10556

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.638 AC: 43344 AN: 67938

Other (OTH) AF: 0.656 AC: 1386 AN: 2112

Alfa AF: 0.636 Hom.: 11962

Bravo AF: 0.647

Asia WGS AF: 0.490 AC: 1703 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.93
DANN	Benign	0.61
PhyloP100		0.081

Splicing

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

Other links and lift over

dbSNP: rs2226844; hg19: chr11-87287439;