XR_007058238.1:n.221-1629T>C

Variant names:

• chr4-114719425-A-G
• rs12510781
• XR_007058238.1:n.221-1629T>C

Variant summary

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

The XR_007058238.1(LOC124900763):​n.221-1629T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0605 in 152,246 control chromosomes in the GnomAD database, including 381 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 0.061 (381 hom., cov: 32)
• Consequence: LOC124900763 XR_007058238.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.57
• Publications: 3 publications found

Genes affected

LOC124900763 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.13 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.0605 AC: 9206 AN: 152128 Hom.: 381 Cov.: 32

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.0672

Gnomad ASJ AF: 0.0715

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.0588

Gnomad FIN AF: 0.0107

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0332

Gnomad OTH AF: 0.0694

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

GnomAD4 genome AF: 0.0605 AC: 9211 AN: 152246 Hom.: 381 Cov.: 32 AF XY: 0.0590 AC XY: 4391 AN XY: 74448

African (AFR) AF: 0.105 AC: 4374 AN: 41550

American (AMR) AF: 0.0673 AC: 1030 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0715 AC: 248 AN: 3470

East Asian (EAS) AF: 0.138 AC: 714 AN: 5172

South Asian (SAS) AF: 0.0588 AC: 284 AN: 4826

European-Finnish (FIN) AF: 0.0107 AC: 113 AN: 10608

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0333 AC: 2262 AN: 68004

Other (OTH) AF: 0.0687 AC: 145 AN: 2110

Alfa AF: 0.0434 Hom.: 349

Bravo AF: 0.0695

Asia WGS AF: 0.110 AC: 382 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.3
DANN	Benign	0.74
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs12510781; hg19: chr4-115640581;