5-67925776-T-G

Variant names:

• chr5-67925776-T-G
• rs12234107
• XR_002956213.2:n.525+95T>G

Variant summary

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

The XR_002956213.2(LOC105379007):​n.525+95T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0977 in 152,204 control chromosomes in the GnomAD database, including 933 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 0.098 (933 hom., cov: 32)
• Consequence: LOC105379007 XR_002956213.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.114
• Publications: 4 publications found

Genes affected

LOC105379007 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.224 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: 0.0978 AC: 14876 AN: 152086 Hom.: 934 Cov.: 32

Gnomad AFR AF: 0.0254

Gnomad AMI AF: 0.0757

Gnomad AMR AF: 0.0750

Gnomad ASJ AF: 0.0609

Gnomad EAS AF: 0.235

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.0744

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.0805

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

GnomAD4 genome AF: 0.0977 AC: 14876 AN: 152204 Hom.: 933 Cov.: 32 AF XY: 0.0966 AC XY: 7186 AN XY: 74422

African (AFR) AF: 0.0253 AC: 1051 AN: 41554

American (AMR) AF: 0.0748 AC: 1143 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0609 AC: 211 AN: 3464

East Asian (EAS) AF: 0.235 AC: 1214 AN: 5166

South Asian (SAS) AF: 0.174 AC: 838 AN: 4818

European-Finnish (FIN) AF: 0.0744 AC: 789 AN: 10602

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.138 AC: 9372 AN: 67998

Other (OTH) AF: 0.0801 AC: 169 AN: 2110

Alfa AF: 0.118 Hom.: 2163

Bravo AF: 0.0925

Asia WGS AF: 0.149 AC: 517 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	3.4
DANN	Benign	0.78
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs12234107; hg19: chr5-67221604;