11-20564617-A-T

Variant names:

• chr11-20564617-A-T
• rs755560
• XR_931105.1:n.87-2925T>A

Variant summary

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

The XR_931105.1(LOC105376584):​n.87-2925T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 152,118 control chromosomes in the GnomAD database, including 3,863 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 0.18 (3863 hom., cov: 32)
• Consequence: LOC105376584 XR_931105.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.170
• Publications: 3 publications found

Genes affected

LOC105376584 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.373 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: 0.176 AC: 26768 AN: 152000 Hom.: 3837 Cov.: 32

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.331

Gnomad SAS AF: 0.0613

Gnomad FIN AF: 0.0802

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0680

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.176 AC: 26847 AN: 152118 Hom.: 3863 Cov.: 32 AF XY: 0.175 AC XY: 12997 AN XY: 74372

African (AFR) AF: 0.378 AC: 15667 AN: 41424

American (AMR) AF: 0.180 AC: 2755 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.166 AC: 576 AN: 3470

East Asian (EAS) AF: 0.332 AC: 1719 AN: 5180

South Asian (SAS) AF: 0.0615 AC: 297 AN: 4826

European-Finnish (FIN) AF: 0.0802 AC: 850 AN: 10602

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0680 AC: 4628 AN: 68014

Other (OTH) AF: 0.149 AC: 315 AN: 2112

Alfa AF: 0.125 Hom.: 277

Bravo AF: 0.198

Asia WGS AF: 0.199 AC: 695 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.2
DANN	Benign	0.75
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs755560; hg19: chr11-20586163;