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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370604	XR_944102.1	n.1596-2084C>A		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;