rs10132223

Variant names:

• chr14-85151040-G-T
• rs10132223
• XR_944102.1:n.1596-2084C>A

Variant summary

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

The XR_944102.1(LOC105370604):​n.1596-2084C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.283 in 150,526 control chromosomes in the GnomAD database, including 7,603 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 0.28 (7603 hom., cov: 31)
• Consequence: LOC105370604 XR_944102.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.514
• Publications: 3 publications found

Genes affected

LOC105370604 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.502 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: 0.282 AC: 42473 AN: 150406 Hom.: 7588 Cov.: 31

Gnomad AFR AF: 0.508

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.0216

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.226

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.283 AC: 42526 AN: 150526 Hom.: 7603 Cov.: 31 AF XY: 0.276 AC XY: 20281 AN XY: 73398

African (AFR) AF: 0.507 AC: 20808 AN: 41002

American (AMR) AF: 0.193 AC: 2902 AN: 15032

Ashkenazi Jewish (ASJ) AF: 0.190 AC: 658 AN: 3462

East Asian (EAS) AF: 0.0214 AC: 109 AN: 5088

South Asian (SAS) AF: 0.121 AC: 573 AN: 4748

European-Finnish (FIN) AF: 0.194 AC: 1973 AN: 10150

Middle Eastern (MID) AF: 0.233 AC: 68 AN: 292

European-Non Finnish (NFE) AF: 0.216 AC: 14648 AN: 67754

Other (OTH) AF: 0.247 AC: 517 AN: 2090

Alfa AF: 0.294 Hom.: 1171

Bravo AF: 0.294

Asia WGS AF: 0.122 AC: 425 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.13
DANN	Benign	0.27
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs10132223; hg19: chr14-85617384;