chr10-29075768-G-A

Variant names:

• chr10-29075768-G-A
• rs10826566
• XR_001747284.1:n.127-3724G>A

Variant summary

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

The XR_001747284.1(LOC107984174):​n.127-3724G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.223 in 152,100 control chromosomes in the GnomAD database, including 4,249 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 0.22 (4249 hom., cov: 33)
• Consequence: LOC107984174 XR_001747284.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00600
• Publications: 6 publications found

Genes affected

LOC107984174 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.338 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.223 AC: 33875 AN: 151982 Hom.: 4243 Cov.: 33

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.351

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.208

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

GnomAD4 genome AF: 0.223 AC: 33914 AN: 152100 Hom.: 4249 Cov.: 33 AF XY: 0.225 AC XY: 16729 AN XY: 74372

African (AFR) AF: 0.333 AC: 13791 AN: 41460

American (AMR) AF: 0.167 AC: 2549 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.204 AC: 707 AN: 3472

East Asian (EAS) AF: 0.351 AC: 1816 AN: 5172

South Asian (SAS) AF: 0.257 AC: 1240 AN: 4818

European-Finnish (FIN) AF: 0.222 AC: 2353 AN: 10580

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.160 AC: 10848 AN: 67998

Other (OTH) AF: 0.211 AC: 446 AN: 2110

Alfa AF: 0.174 Hom.: 3987

Bravo AF: 0.223

Asia WGS AF: 0.304 AC: 1061 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.0
DANN	Benign	0.47
PhyloP100		0.0060

Splicing

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

Other links and lift over

dbSNP: rs10826566; hg19: chr10-29364697;