rs10123453

Variant names:

• chr9-126096907-C-T
• rs10123453
• ENST00000441473.1:n.235+39093C>T

Variant summary

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

The ENST00000441473.1(ENSG00000232413):​n.235+39093C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.307 in 151,944 control chromosomes in the GnomAD database, including 7,657 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 0.31 (7657 hom., cov: 32)
• Consequence: ENSG00000232413 ENST00000441473.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.341
• Publications: 4 publications found

Genes affected

ENSG00000232413 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.384 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000441473.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000232413	ENST00000441473.1	TSL:5	n.235+39093C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.307 AC: 46581 AN: 151826 Hom.: 7642 Cov.: 32

Gnomad AFR AF: 0.390

Gnomad AMI AF: 0.0899

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.227

Gnomad SAS AF: 0.321

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.307 AC: 46627 AN: 151944 Hom.: 7657 Cov.: 32 AF XY: 0.307 AC XY: 22775 AN XY: 74248

African (AFR) AF: 0.389 AC: 16128 AN: 41408

American (AMR) AF: 0.376 AC: 5735 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.223 AC: 774 AN: 3472

East Asian (EAS) AF: 0.227 AC: 1169 AN: 5156

South Asian (SAS) AF: 0.320 AC: 1544 AN: 4818

European-Finnish (FIN) AF: 0.295 AC: 3117 AN: 10568

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.256 AC: 17363 AN: 67934

Other (OTH) AF: 0.301 AC: 636 AN: 2110

Alfa AF: 0.273 Hom.: 3110

Bravo AF: 0.320

Asia WGS AF: 0.270 AC: 940 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.9
DANN	Benign	0.50
PhyloP100		0.34

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: rs10123453;

hg19: chr9-128859186;