11-20564617-A-T

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LOC105376584 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376584	XR_931105.1	n.87-2925T>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.378

Gnomad4 AMR AF: 0.180

Gnomad4 ASJ AF: 0.166

Gnomad4 EAS AF: 0.332

Gnomad4 SAS AF: 0.0615

Gnomad4 FIN AF: 0.0802

Gnomad4 NFE AF: 0.0680

Gnomad4 OTH AF: 0.149

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs755560; hg19: chr11-20586163;