XR_929059.3:n.4052+1317G>C

Variant names:

• chr8-76046714-C-G
• rs1380232
• XR_929059.3:n.4052+1317G>C

Variant summary

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

The XR_929059.3(LOC105375906):​n.4052+1317G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0928 in 152,042 control chromosomes in the GnomAD database, including 985 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 0.093 (985 hom., cov: 32)
• Consequence: LOC105375906 XR_929059.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0400
• Publications: 1 publications found

Genes affected

LOC105375906 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.18 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: 0.0926 AC: 14068 AN: 151924 Hom.: 979 Cov.: 32

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.120

Gnomad SAS AF: 0.0390

Gnomad FIN AF: 0.0212

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0405

Gnomad OTH AF: 0.103

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

GnomAD4 genome AF: 0.0928 AC: 14105 AN: 152042 Hom.: 985 Cov.: 32 AF XY: 0.0916 AC XY: 6805 AN XY: 74326

African (AFR) AF: 0.184 AC: 7605 AN: 41436

American (AMR) AF: 0.124 AC: 1894 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.154 AC: 532 AN: 3462

East Asian (EAS) AF: 0.121 AC: 623 AN: 5168

South Asian (SAS) AF: 0.0384 AC: 185 AN: 4812

European-Finnish (FIN) AF: 0.0212 AC: 225 AN: 10602

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.0405 AC: 2753 AN: 67992

Other (OTH) AF: 0.103 AC: 217 AN: 2104

Alfa AF: 0.0686 Hom.: 73

Bravo AF: 0.108

Asia WGS AF: 0.0980 AC: 342 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.7
DANN	Benign	0.41
PhyloP100		0.040

Splicing

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

Other links and lift over

dbSNP: rs1380232; hg19: chr8-76958949;