14-25440180-T-C

Position:

• chr14-25440180-T-C

Variant summary

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

The XR_002957614.1(LOC112268135):​n.327-3785T>C 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 0.0979 in 152,200 control chromosomes in the GnomAD database, including 1,106 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 0.098 (1106 hom., cov: 32)
• Consequence: LOC112268135 XR_002957614.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.14

Genes affected

LOC112268135 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.391 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC112268135	XR_002957614.1	n.327-3785T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0979 AC: 14896 AN: 152082 Hom.: 1109 Cov.: 32

Gnomad AFR AF: 0.0338

Gnomad AMI AF: 0.0746

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.406

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.0984

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.0979 AC: 14895 AN: 152200 Hom.: 1106 Cov.: 32 AF XY: 0.103 AC XY: 7646 AN XY: 74414

Gnomad4 AFR AF: 0.0339

Gnomad4 AMR AF: 0.120

Gnomad4 ASJ AF: 0.131

Gnomad4 EAS AF: 0.405

Gnomad4 SAS AF: 0.173

Gnomad4 FIN AF: 0.117

Gnomad4 NFE AF: 0.0984

Gnomad4 OTH AF: 0.109

Alfa AF: 0.101 Hom.: 406

Bravo AF: 0.0969

Asia WGS AF: 0.282 AC: 976 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.5
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2332524; hg19: chr14-25909386;