rs10759240

Variant names:

• chr9-107479876-A-C
• rs10759240
• ENST00000837839.1:n.424-394A>C

Variant summary

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

The ENST00000837839.1(ENSG00000309014):​n.424-394A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.609 in 151,694 control chromosomes in the GnomAD database, including 29,879 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 0.61 (29879 hom., cov: 30)
• Consequence: ENSG00000309014 ENST00000837839.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25
• Publications: 4 publications found

Genes affected

ENSG00000309014 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.837 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000837839.1. 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
	ENSG00000309014	ENST00000837839.1		n.424-394A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.609 AC: 92295 AN: 151578 Hom.: 29839 Cov.: 30

Gnomad AFR AF: 0.845

Gnomad AMI AF: 0.348

Gnomad AMR AF: 0.537

Gnomad ASJ AF: 0.633

Gnomad EAS AF: 0.669

Gnomad SAS AF: 0.606

Gnomad FIN AF: 0.569

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.485

Gnomad OTH AF: 0.615

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

GnomAD4 genome AF: 0.609 AC: 92393 AN: 151694 Hom.: 29879 Cov.: 30 AF XY: 0.612 AC XY: 45381 AN XY: 74132

African (AFR) AF: 0.845 AC: 34964 AN: 41398

American (AMR) AF: 0.538 AC: 8187 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.633 AC: 2191 AN: 3460

East Asian (EAS) AF: 0.668 AC: 3439 AN: 5146

South Asian (SAS) AF: 0.606 AC: 2908 AN: 4798

European-Finnish (FIN) AF: 0.569 AC: 5961 AN: 10480

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.485 AC: 32924 AN: 67880

Other (OTH) AF: 0.617 AC: 1297 AN: 2102

Alfa AF: 0.535 Hom.: 61488

Bravo AF: 0.618

Asia WGS AF: 0.649 AC: 2255 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.33
DANN	Benign	0.49
PhyloP100		-1.2

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: rs10759240;

hg19: chr9-110242157;