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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903315	XR_007064164.1	n.633+2055A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;