XR_001739819.1:n.319-24914C>T

Variant names:

• chr2-184408401-C-T
• rs1304514
• XR_001739819.1:n.319-24914C>T

Variant summary

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

The XR_001739819.1(LOC102724340):​n.319-24914C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.396 in 151,950 control chromosomes in the GnomAD database, including 14,303 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 0.40 (14303 hom., cov: 32)
• Consequence: LOC102724340 XR_001739819.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.933
• Publications: 3 publications found

Genes affected

LOC102724340 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.537 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: 0.396 AC: 60090 AN: 151832 Hom.: 14290 Cov.: 32

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.403

Gnomad AMR AF: 0.546

Gnomad ASJ AF: 0.452

Gnomad EAS AF: 0.532

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.454

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.506

Gnomad OTH AF: 0.427

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

GnomAD4 genome AF: 0.396 AC: 60113 AN: 151950 Hom.: 14303 Cov.: 32 AF XY: 0.395 AC XY: 29343 AN XY: 74284

African (AFR) AF: 0.117 AC: 4854 AN: 41490

American (AMR) AF: 0.547 AC: 8328 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.452 AC: 1569 AN: 3468

East Asian (EAS) AF: 0.531 AC: 2737 AN: 5150

South Asian (SAS) AF: 0.425 AC: 2046 AN: 4818

European-Finnish (FIN) AF: 0.454 AC: 4791 AN: 10564

Middle Eastern (MID) AF: 0.473 AC: 138 AN: 292

European-Non Finnish (NFE) AF: 0.506 AC: 34373 AN: 67910

Other (OTH) AF: 0.431 AC: 910 AN: 2110

Alfa AF: 0.380 Hom.: 1837

Bravo AF: 0.396

Asia WGS AF: 0.475 AC: 1652 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.76
DANN	Benign	0.33
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs1304514; hg19: chr2-185273128;