chr10-47205758-C-A

Variant names:

• chr10-47205758-C-A
• rs9421758
• XR_945937.3:n.104-1603C>A

Variant summary

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

The XR_945937.3(LOC105378291):​n.104-1603C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 152,040 control chromosomes in the GnomAD database, including 5,274 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 0.24 (5274 hom., cov: 33)
• Consequence: LOC105378291 XR_945937.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.302
• Publications: 3 publications found

Genes affected

LOC105378291 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.392 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: 0.235 AC: 35762 AN: 151924 Hom.: 5268 Cov.: 33

Gnomad AFR AF: 0.0638

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.408

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.245

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

GnomAD4 genome AF: 0.235 AC: 35766 AN: 152040 Hom.: 5274 Cov.: 33 AF XY: 0.242 AC XY: 17984 AN XY: 74284

African (AFR) AF: 0.0637 AC: 2644 AN: 41502

American (AMR) AF: 0.335 AC: 5117 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.332 AC: 1153 AN: 3470

East Asian (EAS) AF: 0.142 AC: 733 AN: 5168

South Asian (SAS) AF: 0.407 AC: 1957 AN: 4808

European-Finnish (FIN) AF: 0.362 AC: 3815 AN: 10532

Middle Eastern (MID) AF: 0.272 AC: 79 AN: 290

European-Non Finnish (NFE) AF: 0.288 AC: 19560 AN: 67966

Other (OTH) AF: 0.248 AC: 523 AN: 2112

Alfa AF: 0.275 Hom.: 8744

Bravo AF: 0.222

Asia WGS AF: 0.299 AC: 1038 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.8
DANN	Benign	0.68
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs9421758; hg19: chr10-48533604;