rs4078416

Variant names:

• chr14-51290118-A-G
• rs4078416
• XR_007064164.1:n.633+2055A>G

Variant summary

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

The XR_007064164.1(LOC124903315):​n.633+2055A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0369 in 152,282 control chromosomes in the GnomAD database, including 116 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 0.037 (116 hom., cov: 32)
• Consequence: LOC124903315 XR_007064164.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.101
• Publications: 0 publications found

Genes affected

LOC124903315 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0701 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0368 AC: 5599 AN: 152164 Hom.: 116 Cov.: 32

Gnomad AFR AF: 0.0277

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0331

Gnomad ASJ AF: 0.0274

Gnomad EAS AF: 0.0761

Gnomad SAS AF: 0.0626

Gnomad FIN AF: 0.0516

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0369

Gnomad OTH AF: 0.0335

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

GnomAD4 genome AF: 0.0369 AC: 5612 AN: 152282 Hom.: 116 Cov.: 32 AF XY: 0.0380 AC XY: 2831 AN XY: 74464

African (AFR) AF: 0.0277 AC: 1153 AN: 41568

American (AMR) AF: 0.0333 AC: 509 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0274 AC: 95 AN: 3470

East Asian (EAS) AF: 0.0763 AC: 395 AN: 5178

South Asian (SAS) AF: 0.0630 AC: 304 AN: 4822

European-Finnish (FIN) AF: 0.0516 AC: 548 AN: 10614

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0369 AC: 2510 AN: 68016

Other (OTH) AF: 0.0331 AC: 70 AN: 2112

Alfa AF: 0.0368 Hom.: 189

Bravo AF: 0.0344

Asia WGS AF: 0.0680 AC: 236 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.3
DANN	Benign	0.68
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs4078416; hg19: chr14-51756836;