chr5-113963296-C-A

Variant names:

• chr5-113963296-C-A
• rs10519366
• XR_007058906.1:n.2086-34880C>A

Variant summary

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

The XR_007058906.1(LOC124901047):​n.2086-34880C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.206 in 152,050 control chromosomes in the GnomAD database, including 3,529 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 0.21 (3529 hom., cov: 32)
• Consequence: LOC124901047 XR_007058906.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.389
• Publications: 3 publications found

Genes affected

LOC124901047 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.241 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: 0.207 AC: 31380 AN: 151932 Hom.: 3529 Cov.: 32

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.284

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.206 AC: 31382 AN: 152050 Hom.: 3529 Cov.: 32 AF XY: 0.207 AC XY: 15409 AN XY: 74324

African (AFR) AF: 0.129 AC: 5373 AN: 41500

American (AMR) AF: 0.199 AC: 3039 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.223 AC: 773 AN: 3470

East Asian (EAS) AF: 0.162 AC: 834 AN: 5154

South Asian (SAS) AF: 0.233 AC: 1122 AN: 4820

European-Finnish (FIN) AF: 0.284 AC: 3004 AN: 10568

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.244 AC: 16562 AN: 67964

Other (OTH) AF: 0.198 AC: 417 AN: 2110

Alfa AF: 0.222 Hom.: 12020

Bravo AF: 0.196

Asia WGS AF: 0.226 AC: 791 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.66
DANN	Benign	0.48
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs10519366; hg19: chr5-113298993; COSMIC: COSV60184259;