chr10-263586-C-T

Variant names:

• chr10-263586-C-T
• rs3125023
• XR_007062029.1:n.1401G>A

Variant summary

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

The XR_007062029.1(LOC107984191):​n.1401G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.321 in 151,984 control chromosomes in the GnomAD database, including 8,142 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 0.32 (8142 hom., cov: 32)
• Consequence: LOC107984191 XR_007062029.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.766
• Publications: 3 publications found

Genes affected

LOC107984191 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.483 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.321 AC: 48753 AN: 151866 Hom.: 8121 Cov.: 32

Gnomad AFR AF: 0.311

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.312

Gnomad EAS AF: 0.499

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.303

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

GnomAD4 genome AF: 0.321 AC: 48813 AN: 151984 Hom.: 8142 Cov.: 32 AF XY: 0.327 AC XY: 24272 AN XY: 74274

African (AFR) AF: 0.311 AC: 12890 AN: 41426

American (AMR) AF: 0.372 AC: 5688 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.312 AC: 1082 AN: 3470

East Asian (EAS) AF: 0.499 AC: 2572 AN: 5156

South Asian (SAS) AF: 0.364 AC: 1747 AN: 4806

European-Finnish (FIN) AF: 0.384 AC: 4053 AN: 10554

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.293 AC: 19897 AN: 67984

Other (OTH) AF: 0.304 AC: 641 AN: 2112

Alfa AF: 0.241 Hom.: 882

Bravo AF: 0.326

Asia WGS AF: 0.400 AC: 1386 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.2
DANN	Benign	0.66
PhyloP100		-0.77

Splicing

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

Other links and lift over

dbSNP: rs3125023; hg19: chr10-309526;