rs10123453

chr9-126096907-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000441473.1(ENSG00000232413):n.235+39093C>T variant causes a intron, non coding transcript 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: ENST00000441473.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.341

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000441473.1	n.235+39093C>T		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.389

Gnomad4 AMR AF: 0.376

Gnomad4 ASJ AF: 0.223

Gnomad4 EAS AF: 0.227

Gnomad4 SAS AF: 0.320

Gnomad4 FIN AF: 0.295

Gnomad4 NFE AF: 0.256

Gnomad4 OTH AF: 0.301

Alfa AF: 0.268 Hom.: 1984

Bravo AF: 0.320

Asia WGS AF: 0.270 AC: 940 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	2.9
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10123453; hg19: chr9-128859186;