XR_007061686.1:n.455-7123G>A

Variant names:

• chr9-97977842-C-T
• rs4743150
• XR_007061686.1:n.455-7123G>A

Variant summary

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

The XR_007061686.1(LOC124902226):​n.455-7123G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.256 in 152,026 control chromosomes in the GnomAD database, including 5,536 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 0.26 (5536 hom., cov: 33)
• Consequence: LOC124902226 XR_007061686.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.793
• Publications: 35 publications found

Genes affected

LOC124902226 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.471 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: 0.256 AC: 38828 AN: 151908 Hom.: 5530 Cov.: 33

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.490

Gnomad FIN AF: 0.211

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.257

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

GnomAD4 genome AF: 0.256 AC: 38859 AN: 152026 Hom.: 5536 Cov.: 33 AF XY: 0.257 AC XY: 19101 AN XY: 74298

African (AFR) AF: 0.348 AC: 14423 AN: 41446

American (AMR) AF: 0.221 AC: 3379 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.236 AC: 820 AN: 3468

East Asian (EAS) AF: 0.109 AC: 567 AN: 5182

South Asian (SAS) AF: 0.487 AC: 2347 AN: 4820

European-Finnish (FIN) AF: 0.211 AC: 2230 AN: 10546

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.210 AC: 14266 AN: 67960

Other (OTH) AF: 0.259 AC: 547 AN: 2112

Alfa AF: 0.225 Hom.: 14418

Bravo AF: 0.256

Asia WGS AF: 0.323 AC: 1124 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.71
DANN	Benign	0.57
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs4743150; hg19: chr9-100740124;