rs3858029

Variant names:

• chr9-1756470-A-C
• rs3858029
• ENST00000753419.1:n.274+11282T>G

Your query was ambiguous. Multiple possible variants found:

• chr9-1756470-A-C
• chr9-1756470-A-T

Variant summary

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

The ENST00000753419.1(ENSG00000298161):​n.274+11282T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.382 in 151,992 control chromosomes in the GnomAD database, including 11,320 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 0.38 (11320 hom., cov: 32)
• Consequence: ENSG00000298161 ENST00000753419.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75
• Publications: 1 publications found

Genes affected

ENSG00000298161 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.47 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000753419.1. 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
	ENSG00000298161	ENST00000753419.1		n.274+11282T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.381 AC: 57911 AN: 151874 Hom.: 11283 Cov.: 32

Gnomad AFR AF: 0.419

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.459

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.486

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.345

Gnomad OTH AF: 0.378

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

GnomAD4 genome AF: 0.382 AC: 58011 AN: 151992 Hom.: 11320 Cov.: 32 AF XY: 0.386 AC XY: 28652 AN XY: 74286

African (AFR) AF: 0.420 AC: 17401 AN: 41444

American (AMR) AF: 0.460 AC: 7011 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.324 AC: 1125 AN: 3468

East Asian (EAS) AF: 0.486 AC: 2507 AN: 5156

South Asian (SAS) AF: 0.256 AC: 1234 AN: 4818

European-Finnish (FIN) AF: 0.410 AC: 4334 AN: 10564

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.344 AC: 23413 AN: 67966

Other (OTH) AF: 0.382 AC: 809 AN: 2116

Alfa AF: 0.380 Hom.: 1896

Bravo AF: 0.391

Asia WGS AF: 0.412 AC: 1433 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.20
DANN	Benign	0.75
PhyloP100		-1.7

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: rs3858029;

hg19: chr9-1756470;

COSMIC: COSV69442000;