14-25403290-G-T

Variant names:

• chr14-25403290-G-T
• rs17109831
• XR_002957614.1:n.326+26818G>T

Variant summary

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

The XR_002957614.1(LOC112268135):​n.326+26818G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.189 in 152,038 control chromosomes in the GnomAD database, including 3,268 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 0.19 (3268 hom., cov: 32)
• Consequence: LOC112268135 XR_002957614.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.182
• Publications: 0 publications found

Genes affected

LOC112268135 (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 (AFR) allele frequency at 95% confidence interval = 0.301 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.188 AC: 28637 AN: 151922 Hom.: 3249 Cov.: 32

Gnomad AFR AF: 0.305

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0780

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.0796

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.172

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

GnomAD4 genome AF: 0.189 AC: 28701 AN: 152038 Hom.: 3268 Cov.: 32 AF XY: 0.186 AC XY: 13807 AN XY: 74338

African (AFR) AF: 0.305 AC: 12652 AN: 41416

American (AMR) AF: 0.123 AC: 1879 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.110 AC: 382 AN: 3472

East Asian (EAS) AF: 0.00136 AC: 7 AN: 5164

South Asian (SAS) AF: 0.0782 AC: 377 AN: 4818

European-Finnish (FIN) AF: 0.197 AC: 2086 AN: 10592

Middle Eastern (MID) AF: 0.0822 AC: 24 AN: 292

European-Non Finnish (NFE) AF: 0.156 AC: 10616 AN: 67984

Other (OTH) AF: 0.170 AC: 359 AN: 2114

Alfa AF: 0.160 Hom.: 3491

Bravo AF: 0.189

Asia WGS AF: 0.0630 AC: 219 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	3.0
DANN	Benign	0.72
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs17109831; hg19: chr14-25872496;