rs9310784

Variant names:

• chr3-25888713-T-C
• rs9310784
• ENST00000829679.1:n.276+14710T>C

Variant summary

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

The ENST00000829679.1(ENSG00000307904):​n.276+14710T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.201 in 152,136 control chromosomes in the GnomAD database, including 3,718 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 0.20 (3718 hom., cov: 32)
• Consequence: ENSG00000307904 ENST00000829679.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0700
• Publications: 5 publications found

Genes affected

ENSG00000307904 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.33 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000829679.1. 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
	ENSG00000307904	ENST00000829679.1		n.276+14710T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.201 AC: 30557 AN: 152018 Hom.: 3714 Cov.: 32

Gnomad AFR AF: 0.335

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.0399

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.201 AC: 30578 AN: 152136 Hom.: 3718 Cov.: 32 AF XY: 0.200 AC XY: 14841 AN XY: 74390

African (AFR) AF: 0.335 AC: 13881 AN: 41462

American (AMR) AF: 0.140 AC: 2148 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.127 AC: 442 AN: 3470

East Asian (EAS) AF: 0.0394 AC: 204 AN: 5182

South Asian (SAS) AF: 0.252 AC: 1217 AN: 4828

European-Finnish (FIN) AF: 0.156 AC: 1651 AN: 10602

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.154 AC: 10443 AN: 67986

Other (OTH) AF: 0.175 AC: 370 AN: 2114

Alfa AF: 0.161 Hom.: 1815

Bravo AF: 0.205

Asia WGS AF: 0.209 AC: 728 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.0
DANN	Benign	0.67
PhyloP100		-0.070

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: rs9310784;

hg19: chr3-25930204;