rs1255606

Variant names:

• chr11-95472248-A-G
• rs1255606
• XR_947927.2:n.153-2685A>G

Variant summary

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

The XR_947927.2(LOC105369439):​n.153-2685A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.766 in 152,058 control chromosomes in the GnomAD database, including 44,806 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 0.77 (44806 hom., cov: 30)
• Consequence: LOC105369439 XR_947927.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.22
• Publications: 1 publications found

Genes affected

LOC105369439 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.825 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.766 AC: 116353 AN: 151940 Hom.: 44786 Cov.: 30

Gnomad AFR AF: 0.832

Gnomad AMI AF: 0.643

Gnomad AMR AF: 0.716

Gnomad ASJ AF: 0.776

Gnomad EAS AF: 0.749

Gnomad SAS AF: 0.583

Gnomad FIN AF: 0.784

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.749

Gnomad OTH AF: 0.763

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

GnomAD4 genome AF: 0.766 AC: 116419 AN: 152058 Hom.: 44806 Cov.: 30 AF XY: 0.763 AC XY: 56681 AN XY: 74322

African (AFR) AF: 0.832 AC: 34526 AN: 41496

American (AMR) AF: 0.715 AC: 10911 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.776 AC: 2694 AN: 3472

East Asian (EAS) AF: 0.750 AC: 3860 AN: 5150

South Asian (SAS) AF: 0.583 AC: 2808 AN: 4814

European-Finnish (FIN) AF: 0.784 AC: 8280 AN: 10566

Middle Eastern (MID) AF: 0.728 AC: 214 AN: 294

European-Non Finnish (NFE) AF: 0.749 AC: 50935 AN: 67982

Other (OTH) AF: 0.759 AC: 1605 AN: 2116

Alfa AF: 0.757 Hom.: 5312

Bravo AF: 0.767

Asia WGS AF: 0.674 AC: 2345 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.18
DANN	Benign	0.18
PhyloP100		-3.2

Splicing

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

Other links and lift over

dbSNP: rs1255606; hg19: chr11-95205412;