chr4-176480299-G-A

Variant names:

• chr4-176480299-G-A
• rs17063114
• XR_007058376.1:n.1157+29475G>A

Variant summary

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

The XR_007058376.1(LOC124900817):​n.1157+29475G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.363 in 152,024 control chromosomes in the GnomAD database, including 10,352 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 0.36 (10352 hom., cov: 32)
• Consequence: LOC124900817 XR_007058376.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• Publications: 2 publications found

Genes affected

LOC124900817 (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 (AFR) allele frequency at 95% confidence interval = 0.417 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: 0.363 AC: 55206 AN: 151906 Hom.: 10344 Cov.: 32

Gnomad AFR AF: 0.423

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.384

Gnomad ASJ AF: 0.367

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.349

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.363 AC: 55235 AN: 152024 Hom.: 10352 Cov.: 32 AF XY: 0.361 AC XY: 26848 AN XY: 74310

African (AFR) AF: 0.423 AC: 17512 AN: 41448

American (AMR) AF: 0.384 AC: 5860 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.367 AC: 1273 AN: 3470

East Asian (EAS) AF: 0.133 AC: 687 AN: 5176

South Asian (SAS) AF: 0.319 AC: 1535 AN: 4814

European-Finnish (FIN) AF: 0.336 AC: 3553 AN: 10570

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.349 AC: 23690 AN: 67968

Other (OTH) AF: 0.374 AC: 787 AN: 2106

Alfa AF: 0.326 Hom.: 3313

Bravo AF: 0.364

Asia WGS AF: 0.215 AC: 750 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	1.5
DANN	Benign	0.49
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs17063114; hg19: chr4-177401450;