rs11017128

chr10-130191772-A-G

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LOC124902561 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC124902561	XM_047426136.1	c.*547A>G		3_prime_UTR_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.239

Gnomad4 AMR AF: 0.143

Gnomad4 ASJ AF: 0.151

Gnomad4 EAS AF: 0.0785

Gnomad4 SAS AF: 0.0816

Gnomad4 FIN AF: 0.134

Gnomad4 NFE AF: 0.139

Gnomad4 OTH AF: 0.155

Alfa AF: 0.143 Hom.: 1689

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11017128; hg19: chr10-131990036;