XR_925555.1:n.193+302T>G

Variant names:

• chr4-31716823-A-C
• rs10489007
• XR_925555.1:n.193+302T>G

Variant summary

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

The XR_925555.1(LOC105374566):​n.193+302T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 151,738 control chromosomes in the GnomAD database, including 1,076 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 0.10 (1076 hom., cov: 32)
• Consequence: LOC105374566 XR_925555.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.288
• Publications: 2 publications found

Genes affected

LOC105374566 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.143 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: 0.103 AC: 15658 AN: 151620 Hom.: 1076 Cov.: 32

Gnomad AFR AF: 0.0275

Gnomad AMI AF: 0.0329

Gnomad AMR AF: 0.0844

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.0504

Gnomad SAS AF: 0.0910

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.103 AC: 15662 AN: 151738 Hom.: 1076 Cov.: 32 AF XY: 0.104 AC XY: 7697 AN XY: 74154

African (AFR) AF: 0.0275 AC: 1143 AN: 41506

American (AMR) AF: 0.0842 AC: 1279 AN: 15188

Ashkenazi Jewish (ASJ) AF: 0.129 AC: 448 AN: 3460

East Asian (EAS) AF: 0.0507 AC: 261 AN: 5150

South Asian (SAS) AF: 0.0919 AC: 443 AN: 4820

European-Finnish (FIN) AF: 0.180 AC: 1910 AN: 10590

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.146 AC: 9869 AN: 67714

Other (OTH) AF: 0.109 AC: 230 AN: 2104

Alfa AF: 0.136 Hom.: 841

Bravo AF: 0.0940

Asia WGS AF: 0.0840 AC: 293 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.9
DANN	Benign	0.33
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs10489007; hg19: chr4-31718445;