chr14-95703240-A-G

Variant names:

• chr14-95703240-A-G
• rs7159713
• XR_007064320.1:n.539-154A>G

Variant summary

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

The XR_007064320.1(LOC124903373):​n.539-154A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.307 in 152,142 control chromosomes in the GnomAD database, including 11,496 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 0.31 (11496 hom., cov: 32)
• Consequence: LOC124903373 XR_007064320.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.650
• Publications: 15 publications found

Genes affected

LOC124903373 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.678 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: 0.307 AC: 46637 AN: 152024 Hom.: 11458 Cov.: 32

Gnomad AFR AF: 0.684

Gnomad AMI AF: 0.0735

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.245

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

GnomAD4 genome AF: 0.307 AC: 46733 AN: 152142 Hom.: 11496 Cov.: 32 AF XY: 0.307 AC XY: 22839 AN XY: 74400

African (AFR) AF: 0.685 AC: 28398 AN: 41470

American (AMR) AF: 0.217 AC: 3311 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.179 AC: 619 AN: 3464

East Asian (EAS) AF: 0.222 AC: 1147 AN: 5174

South Asian (SAS) AF: 0.217 AC: 1049 AN: 4824

European-Finnish (FIN) AF: 0.226 AC: 2393 AN: 10602

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.135 AC: 9189 AN: 68018

Other (OTH) AF: 0.244 AC: 516 AN: 2112

Alfa AF: 0.180 Hom.: 15481

Bravo AF: 0.320

Asia WGS AF: 0.262 AC: 914 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.059
DANN	Benign	0.60
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs7159713; hg19: chr14-96169577;