rs10988428

Variant names:

• chr9-129576791-G-T
• rs10988428
• ENST00000443993.1:n.190+1193G>T

Variant summary

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

The ENST00000443993.1(ENSG00000227619):​n.190+1193G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0926 in 152,254 control chromosomes in the GnomAD database, including 1,013 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 0.093 (1013 hom., cov: 33)
• Consequence: ENSG00000227619 ENST00000443993.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.719
• Publications: 1 publications found

Genes affected

ENSG00000227619 (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 = 0.206 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000443993.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC105376292	NR_188666.1		n.192+1193G>T		intron	N/A
	LOC105376292	NR_188667.1		n.192+1193G>T		intron	N/A
	LOC105376292	NR_188668.1		n.193-730G>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000227619	ENST00000443993.1	TSL:1	n.190+1193G>T		intron	N/A
	ENSG00000227619	ENST00000650882.1		n.229-730G>T		intron	N/A
	ENSG00000227619	ENST00000658659.1		n.483-730G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0925 AC: 14070 AN: 152136 Hom.: 1011 Cov.: 33

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.0520

Gnomad ASJ AF: 0.0493

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0466

Gnomad FIN AF: 0.0614

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0491

Gnomad OTH AF: 0.0702

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

GnomAD4 genome AF: 0.0926 AC: 14093 AN: 152254 Hom.: 1013 Cov.: 33 AF XY: 0.0911 AC XY: 6778 AN XY: 74440

African (AFR) AF: 0.210 AC: 8706 AN: 41508

American (AMR) AF: 0.0519 AC: 795 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0493 AC: 171 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5186

South Asian (SAS) AF: 0.0464 AC: 224 AN: 4824

European-Finnish (FIN) AF: 0.0614 AC: 652 AN: 10624

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0491 AC: 3336 AN: 68012

Other (OTH) AF: 0.0690 AC: 146 AN: 2116

Alfa AF: 0.0696 Hom.: 189

Bravo AF: 0.0971

Asia WGS AF: 0.0310 AC: 106 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	1.3
DANN	Benign	0.62
PhyloP100		-0.72

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10988428;

hg19: chr9-132339070;