rs11605096

Variant names:

• chr11-113671388-C-A
• rs11605096
• XR_001748390.2:n.5178+9945G>T

Variant summary

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

The XR_001748390.2(LOC107984390):​n.5178+9945G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0807 in 152,148 control chromosomes in the GnomAD database, including 645 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 0.081 (645 hom., cov: 32)
• Consequence: LOC107984390 XR_001748390.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36
• Publications: 1 publications found

Genes affected

LOC107984390 (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 (NFE) allele frequency at 95% confidence interval = 0.114 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: 0.0808 AC: 12278 AN: 152030 Hom.: 644 Cov.: 32

Gnomad AFR AF: 0.0229

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.100

Gnomad ASJ AF: 0.0433

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0673

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.0726

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

GnomAD4 genome AF: 0.0807 AC: 12277 AN: 152148 Hom.: 645 Cov.: 32 AF XY: 0.0791 AC XY: 5882 AN XY: 74378

African (AFR) AF: 0.0228 AC: 947 AN: 41524

American (AMR) AF: 0.0998 AC: 1525 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0433 AC: 150 AN: 3468

East Asian (EAS) AF: 0.00135 AC: 7 AN: 5178

South Asian (SAS) AF: 0.0676 AC: 326 AN: 4824

European-Finnish (FIN) AF: 0.105 AC: 1110 AN: 10580

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.117 AC: 7927 AN: 67984

Other (OTH) AF: 0.0714 AC: 151 AN: 2116

Alfa AF: 0.0926 Hom.: 102

Bravo AF: 0.0753

Asia WGS AF: 0.0360 AC: 126 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	0.18
DANN	Benign	0.50
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs11605096; hg19: chr11-113542110;