rs11017128

Variant names:

• chr10-130191772-A-G
• rs11017128
• XM_047426136.1:c.*547A>G

Variant summary

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

The XM_047426136.1(LOC124902561):​c.*547A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.162 in 151,920 control chromosomes in the GnomAD database, including 2,215 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 0.16 (2215 hom., cov: 33)
• Consequence: LOC124902561 XM_047426136.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.161
• Publications: 10 publications found

Genes affected

LOC124902561 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.235 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: 0.162 AC: 24601 AN: 151802 Hom.: 2209 Cov.: 33

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.0297

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.0779

Gnomad SAS AF: 0.0812

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.162 AC: 24633 AN: 151920 Hom.: 2215 Cov.: 33 AF XY: 0.158 AC XY: 11709 AN XY: 74238

African (AFR) AF: 0.239 AC: 9878 AN: 41412

American (AMR) AF: 0.143 AC: 2183 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.151 AC: 522 AN: 3468

East Asian (EAS) AF: 0.0785 AC: 405 AN: 5160

South Asian (SAS) AF: 0.0816 AC: 393 AN: 4814

European-Finnish (FIN) AF: 0.134 AC: 1413 AN: 10522

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.139 AC: 9442 AN: 67970

Other (OTH) AF: 0.155 AC: 325 AN: 2102

Alfa AF: 0.147 Hom.: 2322

Bravo AF: 0.168

Asia WGS AF: 0.0980 AC: 343 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.016
DANN	Benign	0.33
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs11017128; hg19: chr10-131990036;