rs4740904

Variant names:

• chr9-7682860-G-A
• rs4740904
• ENST00000791473.1:n.247+25100G>A

Variant summary

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

The ENST00000791473.1(ENSG00000303045):​n.247+25100G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.468 in 152,030 control chromosomes in the GnomAD database, including 16,682 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 0.47 (16682 hom., cov: 33)
• Consequence: ENSG00000303045 ENST00000791473.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.19
• Publications: 1 publications found

Genes affected

ENSG00000303045 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.5 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000791473.1. 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
	ENSG00000303045	ENST00000791473.1		n.247+25100G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.467 AC: 71017 AN: 151912 Hom.: 16668 Cov.: 33

Gnomad AFR AF: 0.505

Gnomad AMI AF: 0.621

Gnomad AMR AF: 0.479

Gnomad ASJ AF: 0.531

Gnomad EAS AF: 0.361

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.439

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.448

Gnomad OTH AF: 0.459

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

GnomAD4 genome AF: 0.468 AC: 71085 AN: 152030 Hom.: 16682 Cov.: 33 AF XY: 0.467 AC XY: 34676 AN XY: 74296

African (AFR) AF: 0.505 AC: 20942 AN: 41440

American (AMR) AF: 0.479 AC: 7325 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.531 AC: 1844 AN: 3472

East Asian (EAS) AF: 0.362 AC: 1873 AN: 5170

South Asian (SAS) AF: 0.489 AC: 2358 AN: 4824

European-Finnish (FIN) AF: 0.439 AC: 4631 AN: 10550

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.448 AC: 30459 AN: 67960

Other (OTH) AF: 0.458 AC: 970 AN: 2116

Alfa AF: 0.458 Hom.: 19920

Bravo AF: 0.469

Asia WGS AF: 0.406 AC: 1415 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.021
DANN	Benign	0.53
PhyloP100		-3.2

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: rs4740904;

hg19: chr9-7682860;

COSMIC: COSV69445396;