10-130191772-A-G

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902561	XM_047426136.1	c.*547A>G		3_prime_UTR_variant	Exon 2 of 2		XP_047282092.1

Ensembl

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

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 v4.3

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;