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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC112268135	XR_002957614.1	n.327-3785T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

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 v4.3

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;