rs10026364

Variant names:

• chr4-134601585-C-T
• rs10026364
• XR_939214.2:n.392+14226C>T

Variant summary

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

The XR_939214.2(LOC105377436):​n.392+14226C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0597 in 151,944 control chromosomes in the GnomAD database, including 537 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 0.060 (537 hom., cov: 31)
• Consequence: LOC105377436 XR_939214.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305
• Publications: 7 publications found

Genes affected

LOC105377436 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.154 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: 0.0596 AC: 9050 AN: 151826 Hom.: 538 Cov.: 31

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.0292

Gnomad ASJ AF: 0.0202

Gnomad EAS AF: 0.0240

Gnomad SAS AF: 0.0462

Gnomad FIN AF: 0.0293

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0180

Gnomad OTH AF: 0.0612

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

GnomAD4 genome AF: 0.0597 AC: 9066 AN: 151944 Hom.: 537 Cov.: 31 AF XY: 0.0580 AC XY: 4311 AN XY: 74270

African (AFR) AF: 0.157 AC: 6522 AN: 41452

American (AMR) AF: 0.0291 AC: 442 AN: 15192

Ashkenazi Jewish (ASJ) AF: 0.0202 AC: 70 AN: 3468

East Asian (EAS) AF: 0.0235 AC: 121 AN: 5152

South Asian (SAS) AF: 0.0457 AC: 220 AN: 4818

European-Finnish (FIN) AF: 0.0293 AC: 311 AN: 10610

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0180 AC: 1225 AN: 67932

Other (OTH) AF: 0.0605 AC: 128 AN: 2114

Alfa AF: 0.0355 Hom.: 483

Bravo AF: 0.0645

Asia WGS AF: 0.0470 AC: 163 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.4
DANN	Benign	0.57
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs10026364; hg19: chr4-135522740;