XR_930217.2:n.1287+2113C>T

Variant names:

• chr9-107633792-C-T
• rs11794132
• XR_930217.2:n.1287+2113C>T

Variant summary

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

The XR_930217.2(LOC105376205):​n.1287+2113C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 152,158 control chromosomes in the GnomAD database, including 1,321 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 0.12 (1321 hom., cov: 33)
• Consequence: LOC105376205 XR_930217.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.119
• Publications: 3 publications found

Genes affected

LOC105376205 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.163 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: 0.116 AC: 17684 AN: 152040 Hom.: 1321 Cov.: 33

Gnomad AFR AF: 0.0277

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.0227

Gnomad SAS AF: 0.0938

Gnomad FIN AF: 0.169

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.116 AC: 17695 AN: 152158 Hom.: 1321 Cov.: 33 AF XY: 0.115 AC XY: 8526 AN XY: 74378

African (AFR) AF: 0.0277 AC: 1149 AN: 41538

American (AMR) AF: 0.117 AC: 1785 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.183 AC: 636 AN: 3466

East Asian (EAS) AF: 0.0226 AC: 117 AN: 5180

South Asian (SAS) AF: 0.0943 AC: 455 AN: 4824

European-Finnish (FIN) AF: 0.169 AC: 1786 AN: 10570

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

European-Non Finnish (NFE) AF: 0.166 AC: 11284 AN: 67982

Other (OTH) AF: 0.127 AC: 269 AN: 2112

Alfa AF: 0.152 Hom.: 3139

Bravo AF: 0.106

Asia WGS AF: 0.0650 AC: 224 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.8
DANN	Benign	0.79
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs11794132; hg19: chr9-110396073; COSMIC: COSV62691003;