rs17109831

chr14-25403290-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_002957614.1(LOC112268135):n.326+26818G>T variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.182

Genes affected

LOC112268135 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC112268135	XR_002957614.1	n.326+26818G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.305

Gnomad4 AMR AF: 0.123

Gnomad4 ASJ AF: 0.110

Gnomad4 EAS AF: 0.00136

Gnomad4 SAS AF: 0.0782

Gnomad4 FIN AF: 0.197

Gnomad4 NFE AF: 0.156

Gnomad4 OTH AF: 0.170

Alfa AF: 0.156 Hom.: 2572

Bravo AF: 0.189

Asia WGS AF: 0.0630 AC: 219 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	3.0
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17109831; hg19: chr14-25872496;