rs17096653

Variant names:

• chr14-30389183-A-G
• rs17096653
• XR_007064106.1:n.1276-3053T>C

Variant summary

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

The XR_007064106.1(LOC112267868):​n.1276-3053T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 152,174 control chromosomes in the GnomAD database, including 1,240 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 0.11 (1240 hom., cov: 32)
• Consequence: LOC112267868 XR_007064106.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0980
• Publications: 1 publications found

Genes affected

LOC112267868 (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 (SAS) allele frequency at 95% confidence interval = 0.248 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: 0.110 AC: 16764 AN: 152056 Hom.: 1231 Cov.: 32

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.0230

Gnomad AMR AF: 0.0795

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.0324

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0771

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.110 AC: 16786 AN: 152174 Hom.: 1240 Cov.: 32 AF XY: 0.109 AC XY: 8142 AN XY: 74422

African (AFR) AF: 0.171 AC: 7099 AN: 41454

American (AMR) AF: 0.0794 AC: 1215 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.124 AC: 430 AN: 3468

East Asian (EAS) AF: 0.171 AC: 886 AN: 5180

South Asian (SAS) AF: 0.260 AC: 1253 AN: 4824

European-Finnish (FIN) AF: 0.0324 AC: 344 AN: 10616

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0770 AC: 5240 AN: 68020

Other (OTH) AF: 0.126 AC: 266 AN: 2110

Alfa AF: 0.0991 Hom.: 377

Bravo AF: 0.114

Asia WGS AF: 0.217 AC: 751 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	1.6
DANN	Benign	0.73
PhyloP100		0.098

Splicing

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

Other links and lift over

dbSNP: rs17096653; hg19: chr14-30858389;