rs10511206

Variant names:

• chr10-125530806-C-T
• rs10511206
• XR_946438.2:n.1602C>T

Variant summary

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

The XR_946438.2(LOC105378544):​n.1602C>T 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 0.0942 in 152,298 control chromosomes in the GnomAD database, including 860 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 0.094 (860 hom., cov: 34)
• Consequence: LOC105378544 XR_946438.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0880
• Publications: 2 publications found

Genes affected

LOC105378544 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.214 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: 0.0942 AC: 14339 AN: 152180 Hom.: 857 Cov.: 34

Gnomad AFR AF: 0.0207

Gnomad AMI AF: 0.0976

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.224

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.0942 AC: 14347 AN: 152298 Hom.: 860 Cov.: 34 AF XY: 0.0983 AC XY: 7320 AN XY: 74482

African (AFR) AF: 0.0206 AC: 857 AN: 41572

American (AMR) AF: 0.144 AC: 2197 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.116 AC: 403 AN: 3468

East Asian (EAS) AF: 0.224 AC: 1161 AN: 5178

South Asian (SAS) AF: 0.146 AC: 705 AN: 4824

European-Finnish (FIN) AF: 0.109 AC: 1159 AN: 10604

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.110 AC: 7492 AN: 68026

Other (OTH) AF: 0.117 AC: 247 AN: 2116

Alfa AF: 0.105 Hom.: 484

Bravo AF: 0.0938

Asia WGS AF: 0.219 AC: 762 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.0
DANN	Benign	0.68
PhyloP100		-0.088

Splicing

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

Other links and lift over

dbSNP: rs10511206; hg19: chr10-127219375;