14-25440180-T-C

Variant names:

• chr14-25440180-T-C
• rs2332524
• XR_002957614.1:n.327-3785T>C

Variant summary

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

The XR_002957614.1(LOC112268135):​n.327-3785T>C variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.14
• Publications: 1 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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.391 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: 0.0979 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

African (AFR) AF: 0.0339 AC: 1407 AN: 41550

American (AMR) AF: 0.120 AC: 1832 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.131 AC: 454 AN: 3466

East Asian (EAS) AF: 0.405 AC: 2088 AN: 5152

South Asian (SAS) AF: 0.173 AC: 835 AN: 4814

European-Finnish (FIN) AF: 0.117 AC: 1243 AN: 10612

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.0984 AC: 6692 AN: 67986

Other (OTH) AF: 0.109 AC: 231 AN: 2116

Alfa AF: 0.101 Hom.: 443

Bravo AF: 0.0969

Asia WGS AF: 0.282 AC: 976 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.5
DANN	Benign	0.58
PhyloP100		2.1

Splicing

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

Other links and lift over

dbSNP: rs2332524; hg19: chr14-25909386;