rs11112522

Variant names:

• chr12-105427670-A-G
• rs11112522
• XR_945295.3:n.352+697A>G

Variant summary

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

The XR_945295.3(LOC105369955):​n.352+697A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 152,138 control chromosomes in the GnomAD database, including 1,826 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 0.15 (1826 hom., cov: 32)
• Consequence: LOC105369955 XR_945295.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.393
• Publications: 7 publications found

Genes affected

LOC105369955 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.157 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: 0.150 AC: 22805 AN: 152020 Hom.: 1828 Cov.: 32

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.000962

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.150 AC: 22809 AN: 152138 Hom.: 1826 Cov.: 32 AF XY: 0.150 AC XY: 11138 AN XY: 74380

African (AFR) AF: 0.147 AC: 6093 AN: 41516

American (AMR) AF: 0.160 AC: 2439 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.137 AC: 477 AN: 3472

East Asian (EAS) AF: 0.000965 AC: 5 AN: 5184

South Asian (SAS) AF: 0.146 AC: 706 AN: 4830

European-Finnish (FIN) AF: 0.159 AC: 1680 AN: 10560

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.159 AC: 10829 AN: 67984

Other (OTH) AF: 0.161 AC: 339 AN: 2106

Alfa AF: 0.160 Hom.: 3005

Bravo AF: 0.150

Asia WGS AF: 0.0710 AC: 248 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.4
DANN	Benign	0.73
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs11112522; hg19: chr12-105821448;