4-80237391-G-A

Variant names:

• chr4-80237391-G-A
• rs13149993
• XR_007058161.1:n.80+5105G>A

Variant summary

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

The XR_007058161.1(LOC124900725):​n.80+5105G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.293 in 151,884 control chromosomes in the GnomAD database, including 6,835 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 0.29 (6835 hom., cov: 32)
• Consequence: LOC124900725 XR_007058161.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.286
• Publications: 17 publications found

Genes affected

LOC124900725 (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 = 0.378 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: 0.293 AC: 44452 AN: 151766 Hom.: 6829 Cov.: 32

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.364

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.412

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.318

Gnomad OTH AF: 0.271

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

GnomAD4 genome AF: 0.293 AC: 44470 AN: 151884 Hom.: 6835 Cov.: 32 AF XY: 0.295 AC XY: 21907 AN XY: 74206

African (AFR) AF: 0.215 AC: 8892 AN: 41436

American (AMR) AF: 0.297 AC: 4527 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.241 AC: 833 AN: 3462

East Asian (EAS) AF: 0.393 AC: 2027 AN: 5162

South Asian (SAS) AF: 0.268 AC: 1291 AN: 4820

European-Finnish (FIN) AF: 0.412 AC: 4341 AN: 10534

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.318 AC: 21601 AN: 67900

Other (OTH) AF: 0.269 AC: 567 AN: 2108

Alfa AF: 0.296 Hom.: 8017

Bravo AF: 0.280

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.2
DANN	Benign	0.59
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs13149993; hg19: chr4-81158545;